<?xml version="1.0" encoding="UTF-8"?>
<obo>
<source>
<source_id>obo-all/sequence/sequence.obo</source_id>
<source_type>file</source_type>
<source_fullpath>obo-all/sequence/sequence.obo</source_fullpath>
<source_path>sequence.obo</source_path>
<source_md5>7b760a971c6e38bb839a0f23d16309c4</source_md5>
<source_mtime>1259307450</source_mtime>
<source_parsetime>1259307574</source_parsetime>
</source>
<header>
<format-version>1.2</format-version>
<date>19:11:2009 11:09</date>
<saved-by>kareneilbeck</saved-by>
<auto-generated-by>OBO-Edit 2.1-beta1</auto-generated-by>
<subsetdef>
<id>biosapiens</id>
<name>biosapiens protein feature ontology</name>
</subsetdef>
<subsetdef>
<id>SOFA</id>
<name>SO feature annotation</name>
</subsetdef>
<synonymtypedef>
<id>aa1</id>
<name>amino acid 1 letter code</name>
</synonymtypedef>
<synonymtypedef>
<id>aa3</id>
<name>amino acid 3 letter code</name>
</synonymtypedef>
<synonymtypedef>
<id>AAMOD</id>
<name>amino acid modification</name>
</synonymtypedef>
<synonymtypedef>
<id>BS</id>
<name>biosapiens</name>
</synonymtypedef>
<synonymtypedef>
<id>RNAMOD</id>
<name>RNA modification</name>
<scope>EXACT</scope>
</synonymtypedef>
<default-namespace>sequence</default-namespace>
<remark>autogenerated-by\: DAG-Edit version 1.417\nsaved-by\: eilbeck\ndate\: Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $</remark>
</header>
<term>
<id>SO:0000000</id>
<name>Sequence_Ontology</name>
<subset>SOFA</subset>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000001</id>
<name>region</name>
<def>
<defstr>A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>sequence</synonym_text>
</synonym>
<is_a>SO:0000110</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000002</id>
<name>sequence_secondary_structure</name>
<def>
<defstr>A folded sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>sequence secondary structure</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000003</id>
<name>G_quartet</name>
<def>
<defstr>G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>G quartet</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>G tetrad</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>G-quadruplex</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>G-quartet</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>G-tetrad</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>G_quadruplex</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>guanine tetrad</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/G-quadruplex</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000004</id>
<name>interior_coding_exon</name>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>interior coding exon</synonym_text>
</synonym>
<is_a>SO:0000195</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000005</id>
<name>satellite_DNA</name>
<def>
<defstr>The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>satellite DNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Satellite_DNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000705</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000006</id>
<name>PCR_product</name>
<def>
<defstr>A region amplified by a PCR reaction.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.</comment>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>amplicon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>PCR product</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/RAPD</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000695</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000007</id>
<name>read_pair</name>
<def>
<defstr>A pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.</defstr>
<dbxref>
<acc>ls</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>read-pair</synonym_text>
</synonym>
<is_a>SO:0000143</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000149</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000008</id>
<name>gene_sensu_your_favorite_organism</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000009</id>
<name>gene_class</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000010</id>
<name>protein_coding</name>
<synonym scope="exact">
<synonym_text>protein-coding</synonym_text>
</synonym>
<is_a>SO:0000401</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000011</id>
<name>non_protein_coding</name>
<synonym scope="exact">
<synonym_text>non protein-coding</synonym_text>
</synonym>
<is_a>SO:0000401</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000012</id>
<name>scRNA_primary_transcript</name>
<def>
<defstr>The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>scRNA primary transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>scRNA transcript</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>small cytoplasmic RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>small cytoplasmic RNA transcript</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>small_cytoplasmic_RNA</synonym_text>
</synonym>
<is_a>SO:0000483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000013</id>
<name>scRNA</name>
<def>
<defstr>Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small cytoplasmic RNA</synonym_text>
</synonym>
<is_a>SO:0000655</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000012</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000014</id>
<name>INR_motif</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.</defstr>
<dbxref>
<acc>12651739</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>DMp2</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>initiator</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>initiator motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>INR motif</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000015</id>
<name>DPE_motif</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).</defstr>
<dbxref>
<acc>12651739:12537576</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="narrow">
<synonym_text>CRWMGCGWKCGCTTS</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>downstream core promoter element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DPE motif</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000016</id>
<name>BRE_motif</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.</defstr>
<dbxref>
<acc>12651739</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>B-recognition element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>BRE motif</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>TFIIB recognition element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>transcription factor B-recognition element</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000017</id>
<name>PSE_motif</name>
<def>
<defstr>A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G).</defstr>
<dbxref>
<acc>12651739</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>proximal sequence element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>PSE motif</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000167</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000018</id>
<name>linkage_group</name>
<def>
<defstr>A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.</defstr>
<dbxref>
<acc>038752046</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>linkage group</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Linkage_group</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000020</id>
<name>RNA_internal_loop</name>
<def>
<defstr>A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>RNA internal loop</synonym_text>
</synonym>
<is_a>SO:0000715</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000021</id>
<name>asymmetric_RNA_internal_loop</name>
<def>
<defstr>An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>asymmetric RNA internal loop</synonym_text>
</synonym>
<is_a>SO:0000020</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000022</id>
<name>A_minor_RNA_motif</name>
<def>
<defstr>A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>A minor RNA motif</synonym_text>
</synonym>
<is_a>SO:0000715</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000023</id>
<name>K_turn_RNA_motif</name>
<def>
<defstr>The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>K turn RNA motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>K-turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>kink turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>kink-turn motif</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/K-turn</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000021</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000024</id>
<name>sarcin_like_RNA_motif</name>
<def>
<defstr>A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.</defstr>
<dbxref>
<acc>http://proton.chem.yale.edu/pdf/7897662.pdf</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>sarcin like RNA motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sarcin/ricin domain</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sarcin/ricin loop</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sarcin/ricin RNA domain</synonym_text>
</synonym>
<is_a>SO:0000021</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000025</id>
<name>symmetric_RNA_internal_loop</name>
<def>
<defstr>An internal RNA loop where the extent of the loop on both stands is the same size.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>A-minor RNA motif</synonym_text>
</synonym>
<is_a>SO:0000020</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000026</id>
<name>RNA_junction_loop</name>
<synonym scope="exact">
<synonym_text>RNA junction loop</synonym_text>
</synonym>
<is_a>SO:0000715</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000027</id>
<name>RNA_hook_turn</name>
<synonym scope="related">
<synonym_text>hook turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>hook-turn motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RNA hook turn</synonym_text>
</synonym>
<is_a>SO:0000026</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000028</id>
<name>base_pair</name>
<synonym scope="exact">
<synonym_text>base pair</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Base_pair</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000029</id>
<name>WC_base_pair</name>
<def>
<defstr>The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.</defstr>
<dbxref>
<acc>12177293</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>canonical base pair</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Watson Crick base pair</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>Watson-Crick base pair</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Watson-Crick pair</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>WC base pair</synonym_text>
</synonym>
<is_a>SO:0000028</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000030</id>
<name>sugar_edge_base_pair</name>
<def>
<defstr>A type of non-canonical base-pairing.</defstr>
<dbxref>
<acc>12177293</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>sugar edge base pair</synonym_text>
</synonym>
<is_a>SO:0000028</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000031</id>
<name>aptamer</name>
<def>
<defstr>DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.</defstr>
<dbxref>
<acc>http://aptamer.icmb.utexas.edu</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Aptamer</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000696</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000032</id>
<name>DNA_aptamer</name>
<def>
<defstr>DNA molecules that have been selected from random pools based on their ability to bind other molecules.</defstr>
<dbxref>
<acc>aptamer.icmb.utexas.edu</acc>
<dbname>http</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>DNA aptamer</synonym_text>
</synonym>
<is_a>SO:0000031</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000033</id>
<name>RNA_aptamer</name>
<def>
<defstr>RNA molecules that have been selected from random pools based on their ability to bind other molecules.</defstr>
<dbxref>
<acc>http://aptamer.icmb.utexas.edu</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>RNA aptamer</synonym_text>
</synonym>
<is_a>SO:0000031</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000034</id>
<name>morpholino_oligo</name>
<def>
<defstr>Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.</defstr>
<dbxref>
<acc>http://www.gene-tools.com/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>morpholino oligo</synonym_text>
</synonym>
<is_a>SO:0001247</is_a>
<intersection_of>
<to>SO:0001247</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001183</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000035</id>
<name>riboswitch</name>
<def>
<defstr>A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites.</defstr>
<dbxref>
<acc>2820954</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>riboswitch RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Riboswitch</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000836</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000234</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000036</id>
<name>matrix_attachment_site</name>
<def>
<defstr>A DNA region that is required for the binding of chromatin to the nuclear matrix.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>MAR</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>matrix association region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>matrix attachment region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>matrix attachment site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nuclear matrix association region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nuclear matrix attachment site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>S/MAR</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>S/MAR element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>scaffold attachment site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>scaffold matrix attachment region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>SMAR</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Matrix_attachment_site</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000626</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000037</id>
<name>locus_control_region</name>
<def>
<defstr>A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>LCR</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>locus control element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>locus control region</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Locus_control_region</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000727</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000038</id>
<name>match_set</name>
<def>
<defstr>A collection of match parts.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000039</id>
<name>match_part</name>
<def>
<defstr>A part of a match, for example an hsp from blast is a match_part.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>match part</synonym_text>
</synonym>
<is_a>SO:0001410</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000343</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000040</id>
<name>genomic_clone</name>
<def>
<defstr>A clone of a DNA region of a genome.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>genomic clone</synonym_text>
</synonym>
<is_a>SO:0000151</is_a>
<intersection_of>
<to>SO:0000151</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000991</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000041</id>
<name>sequence_operation</name>
<def>
<defstr>An operation that can be applied to a sequence, that results in a change.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>sequence operation</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000042</id>
<name>pseudogene_attribute</name>
<def>
<defstr>An attribute of a pseudogene (SO:0000336).</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>pseudogene attribute</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000043</id>
<name>processed_pseudogene</name>
<def>
<defstr>A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Please not the synonym R psi M uses the spelled out form of the greek letter.</comment>
<synonym scope="exact">
<synonym_text>processed pseudogene</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>pseudogene by reverse transcription</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>R psi G</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>retropseudogene</synonym_text>
</synonym>
<is_a>SO:0000336</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000044</id>
<name>pseudogene_by_unequal_crossing_over</name>
<def>
<defstr>A pseudogene caused by unequal crossing over at recombination.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>pseudogene by unequal crossing over</synonym_text>
</synonym>
<is_a>SO:0000336</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000045</id>
<name>delete</name>
<def>
<defstr>To remove a subsection of sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000046</id>
<name>insert</name>
<def>
<defstr>To insert a subsection of sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000047</id>
<name>invert</name>
<def>
<defstr>To invert a subsection of sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000048</id>
<name>substitute</name>
<def>
<defstr>To substitute a subsection of sequence for another.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000049</id>
<name>translocate</name>
<def>
<defstr>To translocate a subsection of sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000050</id>
<name>gene_part</name>
<def>
<defstr>A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000051</id>
<name>probe</name>
<def>
<defstr>A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Hybridization_probe</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000696</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000052</id>
<name>assortment_derived_deficiency</name>
<synonym scope="related">
<synonym_text>assortment-derived_deficiency</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000053</id>
<name>sequence_variant_affecting_regulatory_region</name>
<def>
<defstr>A sequence_variant_effect which changes the regulatory region of a gene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting regulatory region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting regulatory region</synonym_text>
</synonym>
<is_a>SO:1000132</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000054</id>
<name>aneuploid</name>
<def>
<defstr>A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Aneuploid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:1000182</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000055</id>
<name>hyperploid</name>
<def>
<defstr>A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Hyperploid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000054</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000056</id>
<name>hypoploid</name>
<def>
<defstr>A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Hypoploid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000054</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000057</id>
<name>operator</name>
<def>
<defstr>A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>operator segment</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Operator_(biology)#Operator</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000752</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000058</id>
<name>assortment_derived_aneuploid</name>
<synonym scope="related">
<synonym_text>assortment-derived_aneuploid</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000059</id>
<name>nuclease_binding_site</name>
<def>
<defstr>A region of a molecule that binds to a nuclease.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>nuclease binding site</synonym_text>
</synonym>
<is_a>SO:0000410</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000060</id>
<name>compound_chromosome_arm</name>
<synonym scope="exact">
<synonym_text>compound chromosome arm</synonym_text>
</synonym>
<is_a>SO:1000042</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000061</id>
<name>restriction_enzyme_binding_site</name>
<def>
<defstr>A region of a molecule that binds to a restriction enzyme.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>restriction endonuclease binding site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>restriction endonuclease recognition site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>restriction enzyme binding site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>restriction enzyme recognition site</synonym_text>
</synonym>
<is_a>SO:0000059</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000062</id>
<name>deficient_intrachromosomal_transposition</name>
<synonym scope="exact">
<synonym_text>deficient intrachromosomal transposition</synonym_text>
</synonym>
<is_a>SO:1000041</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000063</id>
<name>deficient_interchromosomal_transposition</name>
<synonym scope="exact">
<synonym_text>deficient interchromosomal transposition</synonym_text>
</synonym>
<is_a>SO:1000155</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000064</id>
<name>gene_by_transcript_attribute</name>
<comment>This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.</comment>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000065</id>
<name>free_chromosome_arm</name>
<synonym scope="exact">
<synonym_text>free chromosome arm</synonym_text>
</synonym>
<is_a>SO:1000183</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000066</id>
<name>gene_by_polyadenylation_attribute</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000067</id>
<name>gene_to_gene_feature</name>
<synonym scope="exact">
<synonym_text>gene to gene feature</synonym_text>
</synonym>
<is_a>SO:0000401</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000068</id>
<name>overlapping</name>
<def>
<defstr>An attribute describing a gene that has a sequence that overlaps the sequence of another gene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000067</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000069</id>
<name>inside_intron</name>
<def>
<defstr>An attribute to describe a gene when it is located within the intron of another gene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>inside intron</synonym_text>
</synonym>
<is_a>SO:0000068</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000070</id>
<name>inside_intron_antiparallel</name>
<def>
<defstr>An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>inside intron antiparallel</synonym_text>
</synonym>
<is_a>SO:0000069</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000071</id>
<name>inside_intron_parallel</name>
<def>
<defstr>An attribute to describe a gene when it is located within the intron of another gene and on the same strand.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>inside intron parallel</synonym_text>
</synonym>
<is_a>SO:0000069</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000072</id>
<name>end_overlapping_gene</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000073</id>
<name>five_prime_three_prime_overlap</name>
<def>
<defstr>An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>five prime-three prime overlap</synonym_text>
</synonym>
<is_a>SO:0000068</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000074</id>
<name>five_prime_five_prime_overlap</name>
<def>
<defstr>An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>five prime-five prime overlap</synonym_text>
</synonym>
<is_a>SO:0000068</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000075</id>
<name>three_prime_three_prime_overlap</name>
<def>
<defstr>An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>three prime-three prime overlap</synonym_text>
</synonym>
<is_a>SO:0000068</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000076</id>
<name>three_prime_five_prime_overlap</name>
<def>
<defstr>An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5' 3' overlap</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime five prime overlap</synonym_text>
</synonym>
<is_a>SO:0000068</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000077</id>
<name>antisense</name>
<def>
<defstr>A region sequence that is complementary to a sequence of messenger RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Antisense</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000068</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000078</id>
<name>polycistronic_transcript</name>
<def>
<defstr>A transcript that is polycistronic.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>polycistronic transcript</synonym_text>
</synonym>
<is_a>SO:0000673</is_a>
<intersection_of>
<to>SO:0000673</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000880</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000079</id>
<name>dicistronic_transcript</name>
<def>
<defstr>A transcript that is dicistronic.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>dicistronic transcript</synonym_text>
</synonym>
<is_a>SO:0000078</is_a>
<intersection_of>
<to>SO:0000673</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000879</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000080</id>
<name>operon_member</name>
<synonym scope="exact">
<synonym_text>operon member</synonym_text>
</synonym>
<is_a>SO:0000081</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000081</id>
<name>gene_array_member</name>
<synonym scope="exact">
<synonym_text>gene array member</synonym_text>
</synonym>
<is_a>SO:0000401</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000082</id>
<name>processed_transcript_attribute</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000083</id>
<name>macronuclear_sequence</name>
<synonym scope="exact">
<synonym_text>macronuclear sequence</synonym_text>
</synonym>
<is_a>SO:0000736</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000084</id>
<name>micronuclear_sequence</name>
<synonym scope="exact">
<synonym_text>micronuclear sequence</synonym_text>
</synonym>
<is_a>SO:0000736</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000085</id>
<name>gene_by_genome_location</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000086</id>
<name>gene_by_organelle_of_genome</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000087</id>
<name>nuclear_gene</name>
<def>
<defstr>A gene from nuclear sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>nuclear gene</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Nuclear_gene</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000738</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000088</id>
<name>mt_gene</name>
<def>
<defstr>A gene located in mitochondrial sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mitochondrial gene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>mt gene</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Mitochondrial_gene</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000737</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000089</id>
<name>kinetoplast_gene</name>
<def>
<defstr>A gene located in kinetoplast sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>kinetoplast gene</synonym_text>
</synonym>
<is_a>SO:0000088</is_a>
<intersection_of>
<to>SO:0000088</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000741</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000090</id>
<name>plastid_gene</name>
<def>
<defstr>A gene from plastid sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>plastid gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000740</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000091</id>
<name>apicoplast_gene</name>
<def>
<defstr>A gene from apicoplast sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>apicoplast gene</synonym_text>
</synonym>
<is_a>SO:0000090</is_a>
<intersection_of>
<to>SO:0000090</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000743</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000092</id>
<name>ct_gene</name>
<def>
<defstr>A gene from chloroplast sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>chloroplast gene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ct gene</synonym_text>
</synonym>
<is_a>SO:0000090</is_a>
<intersection_of>
<to>SO:0000090</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000745</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000093</id>
<name>chromoplast_gene</name>
<def>
<defstr>A gene from chromoplast_sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>chromoplast gene</synonym_text>
</synonym>
<is_a>SO:0000090</is_a>
<intersection_of>
<to>SO:0000090</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000744</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000094</id>
<name>cyanelle_gene</name>
<def>
<defstr>A gene from cyanelle sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cyanelle gene</synonym_text>
</synonym>
<is_a>SO:0000090</is_a>
<intersection_of>
<to>SO:0000090</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000746</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000095</id>
<name>leucoplast_gene</name>
<def>
<defstr>A plastid gene from leucoplast sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>leucoplast gene</synonym_text>
</synonym>
<is_a>SO:0000090</is_a>
<intersection_of>
<to>SO:0000090</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000747</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000096</id>
<name>proplastid_gene</name>
<def>
<defstr>A gene from proplastid sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>proplastid gene</synonym_text>
</synonym>
<is_a>SO:0000090</is_a>
<intersection_of>
<to>SO:0000090</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000748</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000097</id>
<name>nucleomorph_gene</name>
<def>
<defstr>A gene from nucleomorph sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>nucleomorph gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000739</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000098</id>
<name>plasmid_gene</name>
<def>
<defstr>A gene from plasmid sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>plasmid gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000749</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000099</id>
<name>proviral_gene</name>
<def>
<defstr>A gene from proviral sequence.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>proviral gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000751</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000100</id>
<name>endogenous_retroviral_gene</name>
<def>
<defstr>A proviral gene with origin endogenous retrovirus.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>endogenous retroviral gene</synonym_text>
</synonym>
<is_a>SO:0000099</is_a>
<intersection_of>
<to>SO:0000099</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000903</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000101</id>
<name>transposable_element</name>
<def>
<defstr>A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.</defstr>
<dbxref>
<acc>http://www.sci.sdsu.edu/~smaloy/Glossary/T.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>transposable element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>transposon</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Transposable_element</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001039</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000102</id>
<name>expressed_sequence_match</name>
<def>
<defstr>A match to an EST or cDNA sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>expressed sequence match</synonym_text>
</synonym>
<is_a>SO:0000347</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000103</id>
<name>clone_insert_end</name>
<def>
<defstr>The end of the clone insert.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>clone insert end</synonym_text>
</synonym>
<is_a>SO:0000699</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000753</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000104</id>
<name>polypeptide</name>
<alt_id>SO:0000358</alt_id>
<def>
<defstr>A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequenece_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>protein</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Polypeptide</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000316</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000105</id>
<name>chromosome_arm</name>
<def>
<defstr>A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.</defstr>
<dbxref>
<acc>http://www.medterms.com/script/main/art.asp?articlekey=5152</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>chromosome arm</synonym_text>
</synonym>
<is_a>SO:0000830</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000106</id>
<name>non_capped_primary_transcript</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000107</id>
<name>sequencing_primer</name>
<synonym scope="exact">
<synonym_text>sequencing primer</synonym_text>
</synonym>
<is_a>SO:0000112</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000108</id>
<name>mRNA_with_frameshift</name>
<def>
<defstr>An mRNA with a frameshift.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>frameshifted mRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>mRNA with frameshift</synonym_text>
</synonym>
<is_a>SO:0000234</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000865</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000109</id>
<name>sequence_variant_obs</name>
<def>
<defstr>A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>mutation</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000110</id>
<name>sequence_feature</name>
<def>
<defstr>An extent of biological sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>located sequence feature</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>located_sequence_feature</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence feature</synonym_text>
</synonym>
<disjoint_from>SO:0000240</disjoint_from>
<disjoint_from>SO:0000400</disjoint_from>
<namespace>sequence</namespace>
<is_root>1</is_root>
</term>
<term>
<id>SO:0000111</id>
<name>transposable_element_gene</name>
<def>
<defstr>A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>transposable element gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>OBO_REL:part_of</type>
<to>SO:0000101</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000112</id>
<name>primer</name>
<def>
<defstr>A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase.</defstr>
<dbxref>
<acc>http://www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/glossary.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>DNA primer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>primer oligonucleotide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>primer polynucleotide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>primer sequence</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Primer_(molecular_biology)</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000441</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000113</id>
<name>proviral_region</name>
<def>
<defstr>A viral sequence which has integrated into a host genome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>proviral region</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>proviral sequence</synonym_text>
</synonym>
<is_a>SO:0001039</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000114</id>
<name>methylated_C</name>
<def>
<defstr>A methylated deoxy-cytosine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>methylated C</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>methylated cytosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>methylated cytosine base</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>methylated cytosine residue</synonym_text>
</synonym>
<is_a>SO:0000306</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000115</id>
<name>transcript_feature</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000116</id>
<name>edited</name>
<def>
<defstr>An attribute describing a sequence that is modified by editing.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000117</id>
<name>transcript_with_readthrough_stop_codon</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000118</id>
<name>transcript_with_translational_frameshift</name>
<def>
<defstr>A transcript with a translational frameshift.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>transcript with translational frameshift</synonym_text>
</synonym>
<is_a>SO:0000673</is_a>
<intersection_of>
<to>SO:0000673</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000887</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000119</id>
<name>regulated</name>
<def>
<defstr>An attribute to describe a sequence that is regulated.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000401</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000120</id>
<name>protein_coding_primary_transcript</name>
<def>
<defstr>A primary transcript that, at least in part, encodes one or more proteins.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>May contain introns.</comment>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>pre mRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>protein coding primary transcript</synonym_text>
</synonym>
<is_a>SO:0000185</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000121</id>
<name>forward_primer</name>
<def>
<defstr>A single stranded oligo used for polymerase chain reaction.</defstr>
<dbxref>
<acc>http://mged.sourceforge.net/ontologies/MGEDontology.php</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>DNA forward primer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>forward DNA primer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>forward primer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>forward primer oligo</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>forward primer oligonucleotide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>forward primer polynucleotide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>forward primer sequence</synonym_text>
</synonym>
<is_a>SO:0000112</is_a>
<intersection_of>
<to>SO:0000112</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001030</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000122</id>
<name>RNA_sequence_secondary_structure</name>
<def>
<defstr>A folded RNA sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>RNA sequence secondary structure</synonym_text>
</synonym>
<is_a>SO:0000002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000123</id>
<name>transcriptionally_regulated</name>
<def>
<defstr>An attribute describing a gene that is regulated at transcription.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>By:<protein_id>.</comment>
<synonym scope="exact">
<synonym_text>transcriptionally regulated</synonym_text>
</synonym>
<is_a>SO:0000119</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000124</id>
<name>transcriptionally_constitutive</name>
<def>
<defstr>Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>transcriptionally constitutive</synonym_text>
</synonym>
<is_a>SO:0000123</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000125</id>
<name>transcriptionally_induced</name>
<def>
<defstr>An inducer molecule is required for transcription to occur.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>transcriptionally induced</synonym_text>
</synonym>
<is_a>SO:0000123</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000126</id>
<name>transcriptionally_repressed</name>
<def>
<defstr>A repressor molecule is required for transcription to stop.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>transcriptionally repressed</synonym_text>
</synonym>
<is_a>SO:0000123</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000127</id>
<name>silenced_gene</name>
<def>
<defstr>A gene that is silenced.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>silenced gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000893</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000128</id>
<name>gene_silenced_by_DNA_modification</name>
<def>
<defstr>A gene that is silenced by DNA modification.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene silenced by DNA modification</synonym_text>
</synonym>
<is_a>SO:0000127</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000894</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000129</id>
<name>gene_silenced_by_DNA_methylation</name>
<def>
<defstr>A gene that is silenced by DNA methylation.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene silenced by DNA methylation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>methylation-silenced gene</synonym_text>
</synonym>
<is_a>SO:0000128</is_a>
<intersection_of>
<to>SO:0000128</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000895</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000130</id>
<name>post_translationally_regulated</name>
<def>
<defstr>An attribute describing a gene that is regulated after it has been translated.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>post translationally regulated</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>post-translationally regulated</synonym_text>
</synonym>
<is_a>SO:0000119</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000131</id>
<name>translationally_regulated</name>
<def>
<defstr>An attribute describing a gene that is regulated as it is translated.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>translationally regulated</synonym_text>
</synonym>
<is_a>SO:0000119</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000132</id>
<name>reverse_primer</name>
<def>
<defstr>A single stranded oligo used for polymerase chain reaction.</defstr>
<dbxref>
<acc>http://mged.sourceforge.net/ontologies/MGEDontology.php</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>DNA reverse primer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>reverse DNA primer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>reverse primer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>reverse primer oligo</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>reverse primer oligonucleotide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>reverse primer sequence</synonym_text>
</synonym>
<is_a>SO:0000112</is_a>
<intersection_of>
<to>SO:0000112</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001031</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000133</id>
<name>epigenetically_modified</name>
<def>
<defstr>This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>epigenetically modified</synonym_text>
</synonym>
<is_a>SO:0000401</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000134</id>
<name>imprinted</name>
<def>
<defstr>Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Genomic_imprinting</acc>
<dbname>http</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000119</is_a>
<is_a>SO:0000133</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000135</id>
<name>maternally_imprinted</name>
<def>
<defstr>The maternal copy of the gene is modified, rendering it transcriptionally silent.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>maternally imprinted</synonym_text>
</synonym>
<is_a>SO:0000134</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000136</id>
<name>paternally_imprinted</name>
<def>
<defstr>The paternal copy of the gene is modified, rendering it transcriptionally silent.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>paternally imprinted</synonym_text>
</synonym>
<is_a>SO:0000134</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000137</id>
<name>allelically_excluded</name>
<def>
<defstr>Allelic exclusion is a process occuring in diploid organisms, where a gene is inactivated and not expressed in that cell.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Exapmles are x-innactivation and immunoglobulin formation.</comment>
<synonym scope="exact">
<synonym_text>allelically excluded</synonym_text>
</synonym>
<is_a>SO:0000133</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000138</id>
<name>gene_rearranged_at_DNA_level</name>
<def>
<defstr>An epigenetically modified gene, rearranged at the DNA level.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene rearranged at DNA level</synonym_text>
</synonym>
<is_a>SO:0000898</is_a>
<intersection_of>
<to>SO:0000898</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000904</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000139</id>
<name>ribosome_entry_site</name>
<def>
<defstr>Region in mRNA where ribosome assembles.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>ribosome entry site</synonym_text>
</synonym>
<is_a>SO:0000837</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000203</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000140</id>
<name>attenuator</name>
<def>
<defstr>A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>attenuator sequence</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Attenuator</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0005836</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000234</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000141</id>
<name>terminator</name>
<def>
<defstr>The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>terminator sequence</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Terminator_(genetics)</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0005836</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000673</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000142</id>
<name>DNA_sequence_secondary_structure</name>
<def>
<defstr>A folded DNA sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>DNA sequence secondary structure</synonym_text>
</synonym>
<is_a>SO:0000002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000143</id>
<name>assembly_component</name>
<def>
<defstr>A region of known length which may be used to manufacture a longer region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>assembly component</synonym_text>
</synonym>
<is_a>SO:0001410</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000144</id>
<name>primary_transcript_attribute</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000145</id>
<name>recoded_codon</name>
<def>
<defstr>A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>recoded codon</synonym_text>
</synonym>
<is_a>SO:0000360</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000146</id>
<name>capped</name>
<def>
<defstr>An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000147</id>
<name>exon</name>
<def>
<defstr>A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Exon</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000833</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000148</id>
<name>supercontig</name>
<def>
<defstr>One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.</defstr>
<dbxref>
<acc>ls</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>scaffold</synonym_text>
</synonym>
<is_a>SO:0000353</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000719</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000149</id>
<name>contig</name>
<def>
<defstr>A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unvailable bases.</defstr>
<dbxref>
<acc>ls</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Contig</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000143</is_a>
<is_a>SO:0000353</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000148</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000150</id>
<name>read</name>
<def>
<defstr>A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.</defstr>
<dbxref>
<acc>rd</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_a>SO:0000143</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000149</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000151</id>
<name>clone</name>
<def>
<defstr>A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Clone_(genetics)</acc>
<dbname>http</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000695</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000152</id>
<name>YAC</name>
<def>
<defstr>Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>yeast artificial chromosome</synonym_text>
</synonym>
<is_a>SO:0000440</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000153</id>
<name>BAC</name>
<def>
<defstr>Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>bacterial artificial chromosome</synonym_text>
</synonym>
<is_a>SO:0000440</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000154</id>
<name>PAC</name>
<def>
<defstr>The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.</defstr>
<dbxref>
<acc>http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome.</comment>
<synonym scope="exact">
<synonym_text>P1</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>P1 artificial chromosome</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000440</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000155</id>
<name>plasmid</name>
<def>
<defstr>A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>plasmid sequence</synonym_text>
</synonym>
<is_a>SO:0001235</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000156</id>
<name>cosmid</name>
<def>
<defstr>A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>cosmid vector</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Cosmid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000440</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000157</id>
<name>phagemid</name>
<def>
<defstr>A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>phagemid vector</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Phagemid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000440</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000158</id>
<name>fosmid</name>
<def>
<defstr>A cloning vector that utilises the E. coli F factor.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.</comment>
<synonym scope="related">
<synonym_text>fosmid vector</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Fosmid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000440</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000159</id>
<name>deletion</name>
<alt_id>SO:1000033</alt_id>
<def>
<defstr>The point at which one or more contiguous nucleotides were excised.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>deleted_sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nucleotide deletion</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nucleotide_deletion</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Nucleotide_deletion</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001059</is_a>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000160</id>
<name>lambda_clone</name>
<def>
<defstr>A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.</defstr>
<dbxref>
<acc>0-1767-2380-8</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000161</id>
<name>methylated_A</name>
<def>
<defstr>A modified RNA base in which adenine has been methylated.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>methylated A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>methylated adenine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>methylated adenine base</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>methylated adenine residue</synonym_text>
</synonym>
<is_a>SO:0000306</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000162</id>
<name>splice_site</name>
<def>
<defstr>Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.</defstr>
<dbxref>
<acc>cjm</acc>
<dbname>SO</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>With spliceosomal introns, the splice sites bind the spliceosomal machinary.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>splice site</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Splice_site</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000835</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000163</id>
<name>five_prime_cis_splice_site</name>
<def>
<defstr>Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.</defstr>
<dbxref>
<acc>http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html</acc>
<dbname>URL</dbname>
</dbxref>
<dbxref>
<acc>cjm</acc>
<dbname>SO</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>5' splice site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>donor</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>donor splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>splice donor site</synonym_text>
</synonym>
<is_a>SO:0001419</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000164</id>
<name>three_prime_cis_splice_site</name>
<def>
<defstr>Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.</defstr>
<dbxref>
<acc>http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html</acc>
<dbname>URL</dbname>
</dbxref>
<dbxref>
<acc>cjm</acc>
<dbname>SO</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>3' splice site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>acceptor</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>acceptor splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>splice acceptor site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime splice site</synonym_text>
</synonym>
<is_a>SO:0001419</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000165</id>
<name>enhancer</name>
<def>
<defstr>A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a placeholder should we start to make cross products with GO.</comment>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Enhancer_(genetics)</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000727</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000166</id>
<name>enhancer_bound_by_factor</name>
<def>
<defstr>An enhancer bound by a factor.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>enhancer bound by factor</synonym_text>
</synonym>
<is_a>SO:0000165</is_a>
<intersection_of>
<to>SO:0000165</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000277</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000167</id>
<name>promoter</name>
<def>
<defstr>A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.</defstr>
<dbxref>
<acc>regcreative</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>promoter sequence</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Promoter</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001055</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000168</id>
<name>restriction_enzyme_cut_site</name>
<def>
<defstr>A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000169</id>
<name>RNApol_I_promoter</name>
<def>
<defstr>A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>pol I promoter</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polymerase I promoter</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RNA polymerase A promoter</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RNApol I promoter</synonym_text>
</synonym>
<is_a>SO:0001203</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000170</id>
<name>RNApol_II_promoter</name>
<def>
<defstr>A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>pol II promoter</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polymerase II promoter</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RNA polymerase B promoter</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RNApol II promoter</synonym_text>
</synonym>
<is_a>SO:0000727</is_a>
<is_a>SO:0001203</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000174</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000171</id>
<name>RNApol_III_promoter</name>
<def>
<defstr>A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>pol III promoter</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polymerase III promoter</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RNA polymerase C promoter</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RNApol III promoter</synonym_text>
</synonym>
<is_a>SO:0000727</is_a>
<is_a>SO:0001203</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000174</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000172</id>
<name>CAAT_signal</name>
<def>
<defstr>Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CAAT box</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>CAAT signal</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>CAAT-box</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/CAAT_box</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000173</id>
<name>GC_rich_promoter_region</name>
<def>
<defstr>A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>GC rich promoter region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>GC-rich region</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000174</id>
<name>TATA_box</name>
<def>
<defstr>A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>Goldstein-Hogness box</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>TATA box</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/TATA_box</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000235</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000175</id>
<name>minus_10_signal</name>
<def>
<defstr>A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>-10 signal</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>minus 10 signal</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Pribnow box</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Pribnow Schaller box</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Pribnow-Schaller box</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Pribnow_box</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000613</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000176</id>
<name>minus_35_signal</name>
<def>
<defstr>A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>-35 signal</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>minus 35 signal</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000613</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000177</id>
<name>cross_genome_match</name>
<def>
<defstr>A nucleotide match against a sequence from another organism.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>cross genome match</synonym_text>
</synonym>
<is_a>SO:0000347</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000178</id>
<name>operon</name>
<def>
<defstr>A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Operon</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0005855</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000179</id>
<name>clone_insert_start</name>
<def>
<defstr>The start of the clone insert.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>clone insert start</synonym_text>
</synonym>
<is_a>SO:0000699</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000753</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000180</id>
<name>retrotransposon</name>
<def>
<defstr>A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.</defstr>
<dbxref>
<acc>http://www.dddmag.com/Glossary.aspx#r</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>class I</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>class I transposon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>retrotransposon element</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Retrotransposon</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000101</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000181</id>
<name>translated_nucleotide_match</name>
<def>
<defstr>A match against a translated sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>translated nucleotide match</synonym_text>
</synonym>
<is_a>SO:0000347</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000182</id>
<name>DNA_transposon</name>
<def>
<defstr>A transposon where the mechanism of transposition is via a DNA intermediate.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>class II</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>class II transposon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DNA transposon</synonym_text>
</synonym>
<is_a>SO:0000101</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000183</id>
<name>non_transcribed_region</name>
<def>
<defstr>A region of the gene which is not transcribed.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>non transcribed region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non-transcribed sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nontranscribed region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nontranscribed sequence</synonym_text>
</synonym>
<is_a>SO:0000842</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000184</id>
<name>U2_intron</name>
<def>
<defstr>A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.</defstr>
<dbxref>
<acc>9428511</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>May have either GT-AG or AT-AG 5' and 3' boundaries.</comment>
<synonym scope="exact">
<synonym_text>U2 intron</synonym_text>
</synonym>
<is_a>SO:0000662</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000185</id>
<name>primary_transcript</name>
<def>
<defstr>A transcript that in its initial state requires modification to be functional.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>precursor RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>primary transcript</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Primary_transcript</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000673</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000186</id>
<name>LTR_retrotransposon</name>
<def>
<defstr>A retrotransposon flanked by long terminal repeat sequences.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>long terminal repeat retrotransposon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>LTR retrotransposon</synonym_text>
</synonym>
<is_a>SO:0000180</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000187</id>
<name>repeat_family</name>
<def>
<defstr>A group of characterized repeat sequences.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000188</id>
<name>intron</name>
<def>
<defstr>A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Intron</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000835</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000189</id>
<name>non_LTR_retrotransposon</name>
<def>
<defstr>A retrotransposon without long terminal repeat sequences.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>non LTR retrotransposon</synonym_text>
</synonym>
<is_a>SO:0000180</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000190</id>
<name>five_prime_intron</name>
<synonym scope="exact">
<synonym_text>5' intron</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>5' intron sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime intron</synonym_text>
</synonym>
<is_a>SO:0000188</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000191</id>
<name>interior_intron</name>
<synonym scope="exact">
<synonym_text>interior intron</synonym_text>
</synonym>
<is_a>SO:0000188</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000192</id>
<name>three_prime_intron</name>
<synonym scope="exact">
<synonym_text>3' intron</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>3' intron sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime intron</synonym_text>
</synonym>
<is_a>SO:0000188</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000193</id>
<name>RFLP_fragment</name>
<def>
<defstr>A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.</defstr>
<dbxref>
<acc>pj</acc>
<dbname>GOC</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>restriction fragment length polymorphism</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RFLP</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RFLP fragment</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000412</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000194</id>
<name>LINE_element</name>
<def>
<defstr>A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats.</defstr>
<dbxref>
<acc>http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>LINE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>LINE element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Long interspersed element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Long interspersed nuclear element</synonym_text>
</synonym>
<is_a>SO:0000189</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000195</id>
<name>coding_exon</name>
<def>
<defstr>An exon whereby at least one base is part of a codon (here, 'codon'is inclusive of the stop_codon).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>coding exon</synonym_text>
</synonym>
<is_a>SO:0000147</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000196</id>
<name>five_prime_coding_exon_coding_region</name>
<def>
<defstr>The sequence of the five_prime_coding_exon that codes for protein.</defstr>
<dbxref>
<acc>cjm</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>five prime exon coding region</synonym_text>
</synonym>
<is_a>SO:0001215</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000200</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000197</id>
<name>three_prime_coding_exon_coding_region</name>
<def>
<defstr>The sequence of the three_prime_coding_exon that codes for protein.</defstr>
<dbxref>
<acc>cjm</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>three prime exon coding region</synonym_text>
</synonym>
<is_a>SO:0001215</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000202</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000198</id>
<name>noncoding_exon</name>
<def>
<defstr>An exon that does not contain any codons.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>noncoding exon</synonym_text>
</synonym>
<is_a>SO:0000147</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000199</id>
<name>translocation</name>
<def>
<defstr>A region of nucleotide sequence that has translocated to a new position.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>translocated sequence</synonym_text>
</synonym>
<is_a>SO:0001059</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000200</id>
<name>five_prime_coding_exon</name>
<def>
<defstr>The 5' most coding exon.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>5' coding exon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime coding exon</synonym_text>
</synonym>
<is_a>SO:0000195</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000201</id>
<name>interior_exon</name>
<def>
<defstr>An exon that is bounded by 5' and 3' splice sites.</defstr>
<dbxref>
<acc>10373547</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>interior exon</synonym_text>
</synonym>
<is_a>SO:0000147</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000202</id>
<name>three_prime_coding_exon</name>
<def>
<defstr>The coding exon that is most 3-prime on a given transcript.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>3' coding exon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime coding exon</synonym_text>
</synonym>
<is_a>SO:0000195</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000203</id>
<name>UTR</name>
<def>
<defstr>Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>untranslated region</synonym_text>
</synonym>
<is_a>SO:0000836</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000204</id>
<name>five_prime_UTR</name>
<def>
<defstr>A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>5' UTR</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime UTR</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five_prime_untranslated_region</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/5'_UTR</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000203</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000205</id>
<name>three_prime_UTR</name>
<def>
<defstr>A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>three prime untranslated region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime UTR</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Three_prime_untranslated_region</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000203</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000206</id>
<name>SINE_element</name>
<def>
<defstr>A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>Short interspersed element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Short interspersed nuclear element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>SINE element</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000189</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000207</id>
<name>simple_sequence_length_variation</name>
<synonym scope="related">
<synonym_text>simple sequence length polymorphism</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>simple sequence length variation</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>SSLP</synonym_text>
</synonym>
<is_a>SO:0000248</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000208</id>
<name>terminal_inverted_repeat_element</name>
<def>
<defstr>A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.</defstr>
<dbxref>
<acc>http://www.genetics.org/cgi/reprint/156/4/1983.pdf</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>terminal inverted repeat element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>TIR element</synonym_text>
</synonym>
<is_a>SO:0000182</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000209</id>
<name>rRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a ribosomal RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>ribosomal RNA primary transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000210</id>
<name>tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a transfer RNA (SO:0000253).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000211</id>
<name>alanine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding alanyl tRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>alanine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000212</id>
<name>arginine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding arginyl tRNA (SO:0000255).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>arginine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000213</id>
<name>asparagine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding asparaginyl tRNA (SO:0000256).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>asparagine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000214</id>
<name>aspartic_acid_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding aspartyl tRNA (SO:0000257).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>aspartic acid tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000215</id>
<name>cysteine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding cysteinyl tRNA (SO:0000258).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cysteine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000216</id>
<name>glutamic_acid_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding glutaminyl tRNA (SO:0000260).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>glutamic acid tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000217</id>
<name>glutamine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding glutamyl tRNA (SO:0000260).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>glutamine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000218</id>
<name>glycine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding glycyl tRNA (SO:0000263).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>glycine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000219</id>
<name>histidine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding histidyl tRNA (SO:0000262).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>histidine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000220</id>
<name>isoleucine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding isoleucyl tRNA (SO:0000263).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>isoleucine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000221</id>
<name>leucine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding leucyl tRNA (SO:0000264).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>leucine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000222</id>
<name>lysine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding lysyl tRNA (SO:0000265).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>lysine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000223</id>
<name>methionine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding methionyl tRNA (SO:0000266).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>methionine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000224</id>
<name>phenylalanine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding phenylalanyl tRNA (SO:0000267).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>phenylalanine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000225</id>
<name>proline_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding prolyl tRNA (SO:0000268).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>proline tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000226</id>
<name>serine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding seryl tRNA (SO:000269).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>serine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000227</id>
<name>threonine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding threonyl tRNA (SO:000270).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>threonine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000228</id>
<name>tryptophan_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding tryptophanyl tRNA (SO:000271).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>tryptophan tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000229</id>
<name>tyrosine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding tyrosyl tRNA (SO:000272).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>tyrosine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000230</id>
<name>valine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding valyl tRNA (SO:000273).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>valine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000231</id>
<name>snRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a small nuclear RNA (SO:0000274).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>snRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000232</id>
<name>snoRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a small nucleolar mRNA (SO:0000275).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>snoRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000233</id>
<name>mature_transcript</name>
<def>
<defstr>A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A processed transcript cannot contain introns.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>mature transcript</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Mature_transcript</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000673</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000185</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000234</id>
<name>mRNA</name>
<def>
<defstr>Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>messenger RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/MRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000233</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000235</id>
<name>TF_binding_site</name>
<def>
<defstr>A region of a molecule that binds a TF complex [GO:0005667].</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>TF binding site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>transcription factor binding site</synonym_text>
</synonym>
<is_a>SO:0000410</is_a>
<is_a>SO:0005836</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000236</id>
<name>ORF</name>
<def>
<defstr>The inframe interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.</defstr>
<dbxref>
<acc>rb</acc>
<dbname>SGD</dbname>
</dbxref>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>open reading frame</synonym_text>
</synonym>
<is_a>SO:0000717</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000237</id>
<name>transcript_attribute</name>
<synonym scope="exact">
<synonym_text>transcript attribute</synonym_text>
</synonym>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000238</id>
<name>foldback_element</name>
<def>
<defstr>A transposable element with extensive secondary structure, characterised by large modular imperfect long inverted repeats.</defstr>
<dbxref>
<acc>http://www.genetics.org/cgi/reprint/156/4/1983.pdf</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>foldback element</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>long inverted repeat element</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>LVR element</synonym_text>
</synonym>
<is_a>SO:0000182</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000239</id>
<name>flanking_region</name>
<def>
<defstr>The sequences extending on either side of a specific region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>flanking region</synonym_text>
</synonym>
<is_a>SO:0001412</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000240</id>
<name>chromosome_variation</name>
<synonym scope="exact">
<synonym_text>chromosome variation</synonym_text>
</synonym>
<disjoint_from>SO:0000110</disjoint_from>
<disjoint_from>SO:0000400</disjoint_from>
<disjoint_from>SO:0001060</disjoint_from>
<disjoint_from>SO:1000132</disjoint_from>
<namespace>sequence</namespace>
<is_root>1</is_root>
</term>
<term>
<id>SO:0000241</id>
<name>internal_UTR</name>
<def>
<defstr>A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.</defstr>
<dbxref>
<acc>cjm</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>internal UTR</synonym_text>
</synonym>
<is_a>SO:0000203</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000242</id>
<name>untranslated_region_polycistronic_mRNA</name>
<def>
<defstr>The untranslated sequence separating the 'cistrons' of multicistronic mRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>untranslated region polycistronic mRNA</synonym_text>
</synonym>
<is_a>SO:0000203</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000243</id>
<name>internal_ribosome_entry_site</name>
<def>
<defstr>Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>internal ribosomal entry sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>internal ribosomal entry site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>internal ribosome entry sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>internal ribosome entry site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>IRES</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Internal_ribosome_entry_site</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000139</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000244</id>
<name>four_cutter_restriction_site</name>
<synonym scope="related">
<synonym_text>4-cutter_restriction_site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>four-cutter_restriction_sit</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000245</id>
<name>mRNA_by_polyadenylation_status</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000246</id>
<name>polyadenylated</name>
<def>
<defstr>A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000863</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000247</id>
<name>mRNA_not_polyadenylated</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000248</id>
<name>sequence_length_variation</name>
<synonym scope="exact">
<synonym_text>sequence length variation</synonym_text>
</synonym>
<is_a>SO:1000002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000249</id>
<name>six_cutter_restriction_site</name>
<synonym scope="related">
<synonym_text>6-cutter_restriction_site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>six-cutter_restriction_site</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000250</id>
<name>modified_RNA_base_feature</name>
<def>
<defstr>A post_transcriptionally modified base.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified RNA base feature</synonym_text>
</synonym>
<is_a>SO:0001236</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000251</id>
<name>eight_cutter_restriction_site</name>
<synonym scope="related">
<synonym_text>8-cutter_restriction_site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>eight-cutter_restriction_site</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000252</id>
<name>rRNA</name>
<def>
<defstr>RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
<dbxref>
<acc>0198506732</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>ribosomal ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ribosomal RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/RRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000209</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000253</id>
<name>tRNA</name>
<def>
<defstr>Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005</acc>
<dbname>URL</dbname>
</dbxref>
<dbxref>
<acc>0198506732</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>transfer RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/TRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000210</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000254</id>
<name>alanyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>alanyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>alanyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>alanyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000211</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000255</id>
<name>rRNA_small_subunit_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a small ribosomal subunit RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>rRNA small subunit primary transcript</synonym_text>
</synonym>
<is_a>SO:0000209</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000256</id>
<name>asparaginyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>asparaginyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>asparaginyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>asparaginyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000213</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000257</id>
<name>aspartyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>aspartyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>aspartyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>aspartyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000214</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000258</id>
<name>cysteinyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cysteinyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>cysteinyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>cysteinyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000215</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000259</id>
<name>glutaminyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>glutaminyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>glutaminyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>glutaminyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000216</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000260</id>
<name>glutamyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>glutamyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>glutamyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>glutamyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000217</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000261</id>
<name>glycyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>glycyl tRNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>glycyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>glycyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000218</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000262</id>
<name>histidyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>histidyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>histidyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>histidyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000219</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000263</id>
<name>isoleucyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>isoleucyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>isoleucyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>isoleucyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000220</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000264</id>
<name>leucyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>leucyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>leucyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>leucyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000221</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000265</id>
<name>lysyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>lysyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>lysyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>lysyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000222</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000266</id>
<name>methionyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>methionyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>methionyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>methionyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000223</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000267</id>
<name>phenylalanyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>phenylalanyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>phenylalanyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>phenylalanyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000224</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000268</id>
<name>prolyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a proline anticodon, and a 3' proline binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>prolyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>prolyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>prolyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000225</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000269</id>
<name>seryl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a serine anticodon, and a 3' serine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>seryl tRNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>seryl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>seryl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000226</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000270</id>
<name>threonyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>threonyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>threonyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>threonyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000227</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000271</id>
<name>tryptophanyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>tryptophanyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>tryptophanyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>tryptophanyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000228</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000272</id>
<name>tyrosyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>tyrosyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>tyrosyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>tyrosyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000229</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000273</id>
<name>valyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a valine anticodon, and a 3' valine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>valyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>valyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>valyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000230</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000274</id>
<name>snRNA</name>
<def>
<defstr>A small nuclear RNA molecule involved in pre-mRNA splicing and processing.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
<dbxref>
<acc>11733745</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>ems</acc>
<dbname>WB</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nuclear RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/SnRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000231</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000275</id>
<name>snoRNA</name>
<def>
<defstr>A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.</defstr>
<dbxref>
<acc>kgc</acc>
<dbname>GOC</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nucleolar RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/SnoRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000232</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000276</id>
<name>miRNA</name>
<def>
<defstr>Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.</defstr>
<dbxref>
<acc>12592000</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>micro RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>microRNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/MiRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000370</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000647</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000277</id>
<name>bound_by_factor</name>
<def>
<defstr>An attribute describing a sequence that is bound by another molecule.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Formerly called transcript_by_bound_factor.</comment>
<synonym scope="exact">
<synonym_text>bound by factor</synonym_text>
</synonym>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000278</id>
<name>transcript_bound_by_nucleic_acid</name>
<def>
<defstr>A transcript that is bound by a nucleic acid.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Formerly called transcript_by_bound_nucleic_acid.</comment>
<synonym scope="exact">
<synonym_text>transcript bound by nucleic acid</synonym_text>
</synonym>
<is_a>SO:0000673</is_a>
<intersection_of>
<to>SO:0000673</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000876</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000279</id>
<name>transcript_bound_by_protein</name>
<def>
<defstr>A transcript that is bound by a protein.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Formerly called transcript_by_bound_protein.</comment>
<synonym scope="exact">
<synonym_text>transcript bound by protein</synonym_text>
</synonym>
<is_a>SO:0000673</is_a>
<intersection_of>
<to>SO:0000673</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000875</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000280</id>
<name>engineered_gene</name>
<def>
<defstr>A gene that is engineered.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<is_a>SO:0000804</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000281</id>
<name>engineered_foreign_gene</name>
<def>
<defstr>A gene that is engineered and foreign.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered foreign gene</synonym_text>
</synonym>
<is_a>SO:0000280</is_a>
<is_a>SO:0000285</is_a>
<is_a>SO:0000805</is_a>
<intersection_of>
<to>SO:0000280</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000784</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000282</id>
<name>mRNA_with_minus_1_frameshift</name>
<def>
<defstr>An mRNA with a minus 1 frameshift.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mRNA with minus 1 frameshift</synonym_text>
</synonym>
<is_a>SO:0000108</is_a>
<intersection_of>
<to>SO:0000108</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000866</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000283</id>
<name>engineered_foreign_transposable_element_gene</name>
<def>
<defstr>A transposible_element that is engineered and foreign.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered foreign transposable element gene</synonym_text>
</synonym>
<is_a>SO:0000111</is_a>
<is_a>SO:0000281</is_a>
<intersection_of>
<to>SO:0000111</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000784</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000284</id>
<name>type_I_enzyme_restriction_site</name>
<def>
<defstr>The recognition site is bipartite and interrupted.</defstr>
<dbxref>
<acc>http://www.promega.com</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000285</id>
<name>foreign_gene</name>
<def>
<defstr>A gene that is foreign.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>foreign gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000784</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000286</id>
<name>long_terminal_repeat</name>
<def>
<defstr>A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>direct terminal repeat</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>long terminal repeat</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>LTR</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Long_terminal_repeat</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000657</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000186</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000287</id>
<name>fusion_gene</name>
<def>
<defstr>A gene that is a fusion.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>fusion gene</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Fusion_gene</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000806</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000288</id>
<name>engineered_fusion_gene</name>
<def>
<defstr>A fusion gene that is engineered.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered fusion gene</synonym_text>
</synonym>
<is_a>SO:0000280</is_a>
<is_a>SO:0000287</is_a>
<intersection_of>
<to>SO:0000287</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000289</id>
<name>microsatellite</name>
<def>
<defstr>A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem.</defstr>
<dbxref>
<acc>http://www.informatics.jax.org/silver/glossary.shtml</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>microsatellite locus</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>microsatellite marker</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>VNTR</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Microsatellite</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000005</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000290</id>
<name>dinucleotide_repeat_microsatellite_feature</name>
<synonym scope="exact">
<synonym_text>dinucleotide repeat microsatellite</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>dinucleotide repeat microsatellite feature</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>dinucleotide repeat microsatellite locus</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>dinucleotide repeat microsatellite marker</synonym_text>
</synonym>
<is_a>SO:0000289</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000291</id>
<name>trinucleotide_repeat_microsatellite_feature</name>
<synonym scope="related">
<synonym_text>dinucleotide repeat microsatellite marker</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rinucleotide repeat microsatellite</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>trinucleotide repeat microsatellite feature</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>trinucleotide repeat microsatellite locus</synonym_text>
</synonym>
<is_a>SO:0000289</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000292</id>
<name>repetitive_element</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000293</id>
<name>engineered_foreign_repetitive_element</name>
<def>
<defstr>A repetitive element that is engineered and foreign.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered foreign repetitive element</synonym_text>
</synonym>
<is_a>SO:0000657</is_a>
<is_a>SO:0000805</is_a>
<intersection_of>
<to>SO:0000657</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000784</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000294</id>
<name>inverted_repeat</name>
<def>
<defstr>The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>inverted repeat</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>inverted repeat sequence</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Inverted_repeat</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000657</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000295</id>
<name>U12_intron</name>
<def>
<defstr>A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.</defstr>
<dbxref>
<acc>9428511</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>May have either GT-AC or AT-AC 5' and 3' boundaries.</comment>
<synonym scope="exact">
<synonym_text>U12 intron</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U12-dependent intron</synonym_text>
</synonym>
<is_a>SO:0000662</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000296</id>
<name>origin_of_replication</name>
<def>
<defstr>The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>ori</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>origin of replication</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Origin_of_replication</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0001235</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000297</id>
<name>D_loop</name>
<def>
<defstr>Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>D-loop</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>displacement loop</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/D_loop</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000296</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000298</id>
<name>recombination_feature</name>
<synonym scope="exact">
<synonym_text>recombination feature</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000299</id>
<name>specific_recombination_site</name>
<synonym scope="exact">
<synonym_text>specific recombination site</synonym_text>
</synonym>
<is_a>SO:0000669</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000300</id>
<name>recombination_feature_of_rearranged_gene</name>
<synonym scope="exact">
<synonym_text>recombination feature of rearranged gene</synonym_text>
</synonym>
<is_a>SO:0000299</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000301</id>
<name>vertebrate_immune_system_gene_recombination_feature</name>
<synonym scope="exact">
<synonym_text>vertebrate immune system gene recombination feature</synonym_text>
</synonym>
<is_a>SO:0000300</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000302</id>
<name>J_gene_recombination_feature</name>
<def>
<defstr>Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>J gene recombination feature</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>J-RS</synonym_text>
</synonym>
<is_a>SO:0000939</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000303</id>
<name>clip</name>
<def>
<defstr>Part of the primary transcript that is clipped off during processing.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_a>SO:0000835</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000304</id>
<name>type_II_enzyme_restriction_site</name>
<def>
<defstr>The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site.</defstr>
<dbxref>
<acc>http://www.promega.com</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000305</id>
<name>modified_base_site</name>
<def>
<defstr>A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Modified base:<modified_base>.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>modified base site</synonym_text>
</synonym>
<is_a>SO:0001236</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000306</id>
<name>methylated_base_feature</name>
<def>
<defstr>A nucleotide modified by methylation.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>methylated base feature</synonym_text>
</synonym>
<is_a>SO:0000305</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000307</id>
<name>CpG_island</name>
<def>
<defstr>Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.</defstr>
<dbxref>
<acc>rd</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>CG island</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>CpG island</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/CpG_island</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000308</id>
<name>sequence_feature_locating_method</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000309</id>
<name>computed_feature</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000310</id>
<name>predicted_ab_initio_computation</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000311</id>
<name>computed_feature_by_similarity</name>
<def>
<defstr>.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>similar to:<sequence_id></comment>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000312</id>
<name>experimentally_determined</name>
<def>
<defstr>Attribute to describe a feature that has been experiemntally verified.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>experimentally determined</synonym_text>
</synonym>
<is_a>SO:0000789</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000313</id>
<name>stem_loop</name>
<alt_id>SO:0000019</alt_id>
<def>
<defstr>A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>RNA_hairpin_loop</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>stem loop</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>stem-loop</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Stem_loop</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000122</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000314</id>
<name>direct_repeat</name>
<def>
<defstr>A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>direct repeat</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Direct_repeat</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000657</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000315</id>
<name>TSS</name>
<def>
<defstr>The first base where RNA polymerase begins to synthesize the RNA transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>transcription start site</synonym_text>
</synonym>
<is_a>SO:0000835</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000316</id>
<name>CDS</name>
<def>
<defstr>A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>coding sequence</synonym_text>
</synonym>
<is_a>SO:0000836</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000317</id>
<name>cDNA_clone</name>
<def>
<defstr>Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.</defstr>
<dbxref>
<acc>http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>cDNA clone</synonym_text>
</synonym>
<is_a>SO:0000151</is_a>
<intersection_of>
<to>SO:0000151</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000756</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000318</id>
<name>start_codon</name>
<def>
<defstr>First codon to be translated by a ribosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>initiation codon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>start codon</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Start_codon</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000360</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000319</id>
<name>stop_codon</name>
<def>
<defstr>In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>stop codon</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Stop_codon</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000360</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000320</id>
<name>intronic_splice_enhancer</name>
<def>
<defstr>Sequences within the intron that modulate splice site selection for some introns.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>intronic splice enhancer</synonym_text>
</synonym>
<is_a>SO:0000344</is_a>
<is_a>SO:0000841</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000321</id>
<name>mRNA_with_plus_1_frameshift</name>
<def>
<defstr>An mRNA with a plus 1 frameshift.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mRNA with plus 1 frameshift</synonym_text>
</synonym>
<is_a>SO:0000108</is_a>
<intersection_of>
<to>SO:0000108</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000868</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000322</id>
<name>nuclease_hypersensitive_site</name>
<synonym scope="exact">
<synonym_text>nuclease hypersensitive site</synonym_text>
</synonym>
<is_a>SO:0000684</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000323</id>
<name>coding_start</name>
<def>
<defstr>The first base to be translated into protein.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>coding start</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>translation initiation site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>translation start</synonym_text>
</synonym>
<is_a>SO:0000851</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000324</id>
<name>tag</name>
<def>
<defstr>A nucleotide sequence that may be used to identify a larger sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_a>SO:0000696</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000325</id>
<name>rRNA_large_subunit_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a large ribosomal subunit RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>rRNA large subunit primary transcript</synonym_text>
</synonym>
<is_a>SO:0000209</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000326</id>
<name>SAGE_tag</name>
<def>
<defstr>A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>SAGE tag</synonym_text>
</synonym>
<is_a>SO:0000324</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000327</id>
<name>coding_end</name>
<def>
<defstr>The last base to be translated into protein. It does not include the stop codon.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>coding end</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>translation termination site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>translation_end</synonym_text>
</synonym>
<is_a>SO:0000851</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000328</id>
<name>microarray_oligo</name>
<synonym scope="exact">
<synonym_text>microarray oligo</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>microarray oligonucleotide</synonym_text>
</synonym>
<is_a>SO:0000051</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000329</id>
<name>mRNA_with_plus_2_frameshift</name>
<def>
<defstr>An mRNA with a plus 2 frameshift.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mRNA with plus 2 frameshift</synonym_text>
</synonym>
<is_a>SO:0000108</is_a>
<intersection_of>
<to>SO:0000108</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000869</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000330</id>
<name>conserved_region</name>
<def>
<defstr>Region of sequence similarity by descent from a common ancestor.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>conserved region</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Conserved_region</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001410</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000331</id>
<name>STS</name>
<def>
<defstr>Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.</defstr>
<dbxref>
<acc>http://www.biospace.com</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>sequence tag site</synonym_text>
</synonym>
<is_a>SO:0000324</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000332</id>
<name>coding_conserved_region</name>
<def>
<defstr>Coding region of sequence similarity by descent from a common ancestor.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>coding conserved region</synonym_text>
</synonym>
<is_a>SO:0000330</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000333</id>
<name>exon_junction</name>
<def>
<defstr>The boundary between two exons in a processed transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>exon junction</synonym_text>
</synonym>
<is_a>SO:0000699</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000233</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000334</id>
<name>nc_conserved_region</name>
<def>
<defstr>Non-coding region of sequence similarity by descent from a common ancestor.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>nc conserved region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>noncoding conserved region</synonym_text>
</synonym>
<is_a>SO:0000330</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000335</id>
<name>mRNA_with_minus_2_frameshift</name>
<def>
<defstr>A mRNA with a minus 2 frameshift.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mRNA with minus 2 frameshift</synonym_text>
</synonym>
<is_a>SO:0000108</is_a>
<intersection_of>
<to>SO:0000108</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000867</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000336</id>
<name>pseudogene</name>
<def>
<defstr>A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog).</defstr>
<dbxref>
<acc>http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Pseudogene</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000462</is_a>
<relationship>
<type>non_functional_homolog_of</type>
<to>SO:0000704</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000337</id>
<name>RNAi_reagent</name>
<def>
<defstr>A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.</defstr>
<dbxref>
<acc>rd</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>RNAi reagent</synonym_text>
</synonym>
<is_a>SO:0000442</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000338</id>
<name>MITE</name>
<def>
<defstr>A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins.</defstr>
<dbxref>
<acc>http://www.pnas.org/cgi/content/full/97/18/10083</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>miniature inverted repeat transposable element</synonym_text>
</synonym>
<is_a>SO:0000208</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000339</id>
<name>recombination_hotspot</name>
<def>
<defstr>A region in a genome which promotes recombination.</defstr>
<dbxref>
<acc>rd</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>recombination hotspot</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Recombination_hotspot</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000298</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000340</id>
<name>chromosome</name>
<def>
<defstr>Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Chromosome</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001235</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000341</id>
<name>chromosome_band</name>
<def>
<defstr>A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>chromosome band</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>cytoband</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>cytological band</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Cytological_band</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000830</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000342</id>
<name>site_specific_recombination_target_region</name>
<synonym scope="exact">
<synonym_text>site specific recombination target region</synonym_text>
</synonym>
<is_a>SO:0000299</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000343</id>
<name>match</name>
<def>
<defstr>A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_a>SO:0001410</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000344</id>
<name>splice_enhancer</name>
<def>
<defstr>Region of a transcript that regulates splicing.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>splice enhancer</synonym_text>
</synonym>
<is_a>SO:0001056</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000345</id>
<name>EST</name>
<def>
<defstr>A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>expressed sequence tag</synonym_text>
</synonym>
<is_a>SO:0000324</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000234</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000346</id>
<name>loxP_site</name>
<synonym scope="related">
<synonym_text>Cre-recombination target region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>loxP site</synonym_text>
</synonym>
<is_a>SO:0000947</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000347</id>
<name>nucleotide_match</name>
<def>
<defstr>A match against a nucleotide sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>nucleotide match</synonym_text>
</synonym>
<is_a>SO:0000343</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000348</id>
<name>nucleic_acid</name>
<def>
<defstr>An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.</defstr>
<dbxref>
<acc>33696</acc>
<dbname>CHEBI</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>nucleic acid</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Nucleic_acid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000443</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000349</id>
<name>protein_match</name>
<def>
<defstr>A match against a protein sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>protein match</synonym_text>
</synonym>
<is_a>SO:0000343</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000350</id>
<name>FRT_site</name>
<def>
<defstr>An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>FLP recombination target region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>FRT site</synonym_text>
</synonym>
<is_a>SO:0000948</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000351</id>
<name>synthetic_sequence</name>
<def>
<defstr>An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>synthetic sequence</synonym_text>
</synonym>
<is_a>SO:0000443</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000352</id>
<name>DNA</name>
<def>
<defstr>An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<is_a>SO:0000348</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000353</id>
<name>sequence_assembly</name>
<def>
<defstr>A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>sequence assembly</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Sequence_assembly</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001248</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000354</id>
<name>group_1_intron_homing_endonuclease_target_region</name>
<synonym scope="exact">
<synonym_text>group 1 intron homing endonuclease target region</synonym_text>
</synonym>
<is_a>SO:0000684</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000355</id>
<name>haplotype_block</name>
<def>
<defstr>A region of the genome which is co-inherited as the result of the lack of historic recombination within it.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>haplotype block</synonym_text>
</synonym>
<is_a>SO:0000298</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000356</id>
<name>RNA</name>
<def>
<defstr>An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<is_a>SO:0000348</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000357</id>
<name>flanked</name>
<def>
<defstr>An attribute describing a region that is bounded either side by a paricular kind of region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000359</id>
<name>floxed</name>
<def>
<defstr>An attribute describing sequence that is flanked by Lox-P sites.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Floxed</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000357</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000360</id>
<name>codon</name>
<def>
<defstr>A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.</defstr>
<dbxref>
<acc>http://www.everythingbio.com/glos/definition.php?word=codon</acc>
<dbname>URL</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Codon</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000851</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000361</id>
<name>FRT_flanked</name>
<def>
<defstr>An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>FRT flanked</synonym_text>
</synonym>
<is_a>SO:0000357</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000362</id>
<name>invalidated_by_chimeric_cDNA</name>
<def>
<defstr>A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>invalidated by chimeric cDNA</synonym_text>
</synonym>
<is_a>SO:0000790</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000363</id>
<name>floxed_gene</name>
<def>
<defstr>A transgene that is floxed.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>floxed gene</synonym_text>
</synonym>
<is_a>SO:0000902</is_a>
<intersection_of>
<to>SO:0000902</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000359</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000364</id>
<name>transposable_element_flanking_region</name>
<def>
<defstr>The region of sequence surrounding a transposible element.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>transposable element flanking region</synonym_text>
</synonym>
<is_a>SO:0000239</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000365</id>
<name>integron</name>
<def>
<defstr>A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Integron</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001039</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000366</id>
<name>insertion_site</name>
<def>
<defstr>The junction where an insertion occurred.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>insertion site</synonym_text>
</synonym>
<is_a>SO:0000699</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000367</id>
<name>attI_site</name>
<def>
<defstr>A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>attI site</synonym_text>
</synonym>
<is_a>SO:0000946</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000365</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000368</id>
<name>transposable_element_insertion_site</name>
<def>
<defstr>The junction in a genome where a transposable_element has inserted.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>transposable element insertion site</synonym_text>
</synonym>
<is_a>SO:0000366</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000369</id>
<name>integrase_coding_region</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000370</id>
<name>small_regulatory_ncRNA</name>
<def>
<defstr>A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small regulatory ncRNA</synonym_text>
</synonym>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000371</id>
<name>conjugative_transposon</name>
<def>
<defstr>A transposon that encodes function required for conjugation.</defstr>
<dbxref>
<acc>http://www.sci.sdsu.edu/~smaloy/Glossary/C.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>conjugative transposon</synonym_text>
</synonym>
<is_a>SO:0000182</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000372</id>
<name>enzymatic_RNA</name>
<def>
<defstr>An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>enzymatic RNA</synonym_text>
</synonym>
<is_a>SO:0000673</is_a>
<intersection_of>
<to>SO:0000673</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001185</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000373</id>
<name>recombinationally_inverted_gene</name>
<def>
<defstr>A recombinationally rearranged gene by inversion.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>recombinationally inverted gene</synonym_text>
</synonym>
<is_a>SO:0000456</is_a>
<intersection_of>
<to>SO:0000456</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:1000036</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000374</id>
<name>ribozyme</name>
<def>
<defstr>An RNA with catalytic activity.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Ribozyme</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000372</is_a>
<intersection_of>
<to>SO:0000372</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001186</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000375</id>
<name>rRNA_5_8S</name>
<def>
<defstr>5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>5.8S LSU rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>5.8S ribosomal RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>5.8S rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rRNA 5 8S</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000651</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000376</id>
<name>RNA_6S</name>
<def>
<defstr>A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>6S RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RNA 6S</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/6S_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000370</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000377</id>
<name>CsrB_RsmB_RNA</name>
<def>
<defstr>An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CsrB RsmB RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>CsrB-RsmB RNA</synonym_text>
</synonym>
<is_a>SO:0000370</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000378</id>
<name>DsrA_RNA</name>
<def>
<defstr>DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>DsrA RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/DsrA_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000370</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000379</id>
<name>GcvB_RNA</name>
<def>
<defstr>A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>GcvB RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/GcvB_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000378</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000380</id>
<name>hammerhead_ribozyme</name>
<def>
<defstr>A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.</defstr>
<dbxref>
<acc>http://rnaworld.bio.ku.edu/class/RNA/RNA00/RNA_World_3.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>hammerhead ribozyme</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Hammerhead_ribozyme</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000715</is_a>
<intersection_of>
<to>SO:0000715</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001186</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000381</id>
<name>group_IIA_intron</name>
<synonym scope="exact">
<synonym_text>group IIA intron</synonym_text>
</synonym>
<is_a>SO:0000603</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000382</id>
<name>group_IIB_intron</name>
<synonym scope="exact">
<synonym_text>group IIB intron</synonym_text>
</synonym>
<is_a>SO:0000603</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000383</id>
<name>MicF_RNA</name>
<def>
<defstr>A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>MicF RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/MicF_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000644</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000384</id>
<name>OxyS_RNA</name>
<def>
<defstr>A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>OxyS RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/OxyS_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000370</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000385</id>
<name>RNase_MRP_RNA</name>
<def>
<defstr>The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>RNase MRP RNA</synonym_text>
</synonym>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000386</id>
<name>RNase_P_RNA</name>
<def>
<defstr>The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterised activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>RNase P RNA</synonym_text>
</synonym>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000387</id>
<name>RprA_RNA</name>
<def>
<defstr>Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>RprA RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/RprA_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000370</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000388</id>
<name>RRE_RNA</name>
<def>
<defstr>The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>RRE RNA</synonym_text>
</synonym>
<is_a>SO:0000370</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000389</id>
<name>spot_42_RNA</name>
<def>
<defstr>A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>spot-42 RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Spot_42_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000370</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000390</id>
<name>telomerase_RNA</name>
<def>
<defstr>The RNA component of telomerase, a reverse transcriptase that synthesises telomeric DNA.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>telomerase RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Telomerase_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000391</id>
<name>U1_snRNA</name>
<def>
<defstr>U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nuclear RNA U1</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>snRNA U1</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U1 small nuclear RNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U1 snRNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/U1_snRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000392</id>
<name>U2_snRNA</name>
<def>
<defstr>U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nuclear RNA U2</synonym_text>
<dbxref>
<acc>CB</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>snRNA U2</synonym_text>
<dbxref>
<acc>CB</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U2 small nuclear RNA</synonym_text>
<dbxref>
<acc>CB</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U2 snRNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/U2_snRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000393</id>
<name>U4_snRNA</name>
<def>
<defstr>U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nuclear RNA U4</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>snRNA U4</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U4 small nuclear RNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U4 snRNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/U4_snRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000394</id>
<name>U4atac_snRNA</name>
<def>
<defstr>An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).</defstr>
<dbxref>
<acc>=12409455</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nuclear RNA U4atac</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>snRNA U4atac</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U4atac small nuclear RNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U4atac snRNA</synonym_text>
</synonym>
<is_a>SO:0000274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000395</id>
<name>U5_snRNA</name>
<def>
<defstr>U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nuclear RNA U5</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>snRNA U5</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U5 small nuclear RNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U5 snRNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/U5_snRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000396</id>
<name>U6_snRNA</name>
<def>
<defstr>U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nuclear RNA U6</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>snRNA U6</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U6 small nuclear RNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U6 snRNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/U6_snRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000397</id>
<name>U6atac_snRNA</name>
<def>
<defstr>U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>snRNA U6atac</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U6atac small nuclear RNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U6atac snRNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<is_a>SO:0000274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000398</id>
<name>U11_snRNA</name>
<def>
<defstr>U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.</defstr>
<dbxref>
<acc>9622129</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nuclear RNA U11</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>snRNA U11</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U11 small nuclear RNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U11 snRNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/U11_snRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000399</id>
<name>U12_snRNA</name>
<def>
<defstr>The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nuclear RNA U12</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>snRNA U12</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U12 small nuclear RNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>U12 snRNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/U12_snRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000400</id>
<name>sequence_attribute</name>
<def>
<defstr>An attribute describes a quality of sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>sequence attribute</synonym_text>
</synonym>
<disjoint_from>SO:0000110</disjoint_from>
<disjoint_from>SO:0000240</disjoint_from>
<disjoint_from>SO:0001060</disjoint_from>
<disjoint_from>SO:1000132</disjoint_from>
<namespace>sequence</namespace>
<is_root>1</is_root>
</term>
<term>
<id>SO:0000401</id>
<name>gene_attribute</name>
<synonym scope="exact">
<synonym_text>gene attribute</synonym_text>
</synonym>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000402</id>
<name>enhancer_attribute</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000403</id>
<name>U14_snoRNA</name>
<alt_id>SO:0005839</alt_id>
<def>
<defstr>U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016</acc>
<dbname>URL</dbname>
</dbxref>
<dbxref>
<acc>2551119</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small nucleolar RNA U14</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>snoRNA U14</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U14 small nucleolar RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U14 snoRNA</synonym_text>
</synonym>
<is_a>SO:0000593</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0005837</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000404</id>
<name>vault_RNA</name>
<def>
<defstr>A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>vault RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Vault_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000405</id>
<name>Y_RNA</name>
<def>
<defstr>Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>Y RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Y_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000406</id>
<name>twintron</name>
<def>
<defstr>An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.</defstr>
<dbxref>
<acc>1899376</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>7823908</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Twintron</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000188</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000407</id>
<name>rRNA_18S</name>
<def>
<defstr>A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>18S ribosomal RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>18S rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rRNA 18S</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/18S_ribosomal_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000650</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000408</id>
<name>site</name>
<def>
<defstr>The interbase position where something (eg an aberration) occurred.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000409</id>
<name>binding_site</name>
<alt_id>BS:00033</alt_id>
<def>
<defstr>A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>binding_or_interaction_site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>site</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Binding_site</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000410</id>
<name>protein_binding_site</name>
<def>
<defstr>A region of a molecule that binds to a protein.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>protein binding site</synonym_text>
</synonym>
<is_a>SO:0000409</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000411</id>
<name>rescue_region</name>
<def>
<defstr>A region that rescues.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>rescue fragment</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rescue region</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>rescue segment</synonym_text>
</synonym>
<is_a>SO:0000695</is_a>
<intersection_of>
<to>SO:0000695</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000814</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000412</id>
<name>restriction_fragment</name>
<def>
<defstr>A region of polynucleotide sequence produced by digestion with a restriction endonuclease.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>restriction fragment</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Restriction_fragment</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000143</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000413</id>
<name>sequence_difference</name>
<def>
<defstr>A region where the sequence differs from that of a specified sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>sequence difference</synonym_text>
</synonym>
<is_a>SO:0000700</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000414</id>
<name>invalidated_by_genomic_contamination</name>
<def>
<defstr>An attribute to describe a feature that is invalidated due to genomic contamination.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>invalidated by genomic contamination</synonym_text>
</synonym>
<is_a>SO:0000790</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000415</id>
<name>invalidated_by_genomic_polyA_primed_cDNA</name>
<def>
<defstr>An attribute to describe a feature that is invalidated due to polyA priming.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>invalidated by genomic polyA primed cDNA</synonym_text>
</synonym>
<is_a>SO:0000790</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000416</id>
<name>invalidated_by_partial_processing</name>
<def>
<defstr>An attribute to describe a feature that is invalidated due to partial processing.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>invalidated by partial processing</synonym_text>
</synonym>
<is_a>SO:0000790</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000417</id>
<name>polypeptide_domain</name>
<alt_id>BS:00012</alt_id>
<alt_id>BS:00134</alt_id>
<alt_id>SO:0001069</alt_id>
<def>
<defstr>A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.</comment>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>ca_bind</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>DNA_bind</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym synonym_type="BS" scope="broad">
<synonym_text>domain</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>np_bind</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide domain</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="exact">
<synonym_text>polypeptide_structural_domain</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="broad">
<synonym_text>structural domain</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>zn_fing</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<is_a>SO:0001070</is_a>
<is_a>SO:0100021</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000418</id>
<name>signal_peptide</name>
<alt_id>BS:00159</alt_id>
<def>
<defstr>The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.</comment>
<subset>biosapiens</subset>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>signal</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>signal peptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>signal peptide coding sequence</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Signal_peptide</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0100011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000419</id>
<name>mature_protein_region</name>
<alt_id>BS:00149</alt_id>
<def>
<defstr>The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.</comment>
<subset>biosapiens</subset>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>chain</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="related">
<synonym_text>mature peptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>mature protein region</synonym_text>
</synonym>
<is_a>SO:0000839</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0001063</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000420</id>
<name>five_prime_terminal_inverted_repeat</name>
<synonym scope="exact">
<synonym_text>5' TIR</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime terminal inverted repeat</synonym_text>
</synonym>
<is_a>SO:0000481</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000421</id>
<name>three_prime_terminal_inverted_repeat</name>
<synonym scope="exact">
<synonym_text>3' TIR</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime terminal inverted repeat</synonym_text>
</synonym>
<is_a>SO:0000481</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000422</id>
<name>U5_LTR_region</name>
<synonym scope="exact">
<synonym_text>U5 long terminal repeat region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U5 LTR region</synonym_text>
</synonym>
<is_a>SO:0000848</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000423</id>
<name>R_LTR_region</name>
<synonym scope="exact">
<synonym_text>R long terminal repeat region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>R LTR region</synonym_text>
</synonym>
<is_a>SO:0000848</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000424</id>
<name>U3_LTR_region</name>
<synonym scope="exact">
<synonym_text>U3 long terminal repeat region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U3 LTR region</synonym_text>
</synonym>
<is_a>SO:0000848</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000425</id>
<name>five_prime_LTR</name>
<synonym scope="exact">
<synonym_text>5' long terminal repeat</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>5' LTR</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime LTR</synonym_text>
</synonym>
<is_a>SO:0000286</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000426</id>
<name>three_prime_LTR</name>
<synonym scope="exact">
<synonym_text>3' long terminal repeat</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>3' LTR</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime LTR</synonym_text>
</synonym>
<is_a>SO:0000286</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000427</id>
<name>R_five_prime_LTR_region</name>
<synonym scope="exact">
<synonym_text>R 5' long term repeat region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>R five prime LTR region</synonym_text>
</synonym>
<is_a>SO:0000423</is_a>
<is_a>SO:0000850</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000428</id>
<name>U5_five_prime_LTR_region</name>
<synonym scope="exact">
<synonym_text>U5 5' long terminal repeat region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U5 five prime LTR region</synonym_text>
</synonym>
<is_a>SO:0000422</is_a>
<is_a>SO:0000850</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000429</id>
<name>U3_five_prime_LTR_region</name>
<synonym scope="exact">
<synonym_text>U3 5' long term repeat region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U3 five prime LTR region</synonym_text>
</synonym>
<is_a>SO:0000424</is_a>
<is_a>SO:0000850</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000430</id>
<name>R_three_prime_LTR_region</name>
<synonym scope="exact">
<synonym_text>R 3' long terminal repeat region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>R three prime LTR region</synonym_text>
</synonym>
<is_a>SO:0000849</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000431</id>
<name>U3_three_prime_LTR_region</name>
<synonym scope="exact">
<synonym_text>U3 3' long terminal repeat region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U3 three prime LTR region</synonym_text>
</synonym>
<is_a>SO:0000849</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000432</id>
<name>U5_three_prime_LTR_region</name>
<synonym scope="exact">
<synonym_text>U5 3' long terminal repeat region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U5 three prime LTR region</synonym_text>
</synonym>
<is_a>SO:0000849</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000433</id>
<name>non_LTR_retrotransposon_polymeric_tract</name>
<def>
<defstr>A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>non LTR retrotransposon polymeric tract</synonym_text>
</synonym>
<is_a>SO:0000657</is_a>
<is_a>SO:0000840</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000189</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000434</id>
<name>target_site_duplication</name>
<def>
<defstr>A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.</defstr>
<dbxref>
<acc>http://www.koko.gov.my/CocoaBioTech/Glossaryt.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>target site duplication</synonym_text>
</synonym>
<is_a>SO:0000314</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000435</id>
<name>RR_tract</name>
<def>
<defstr>A polypurine tract within an LTR_retrotransposon.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>LTR retrotransposon poly purine tract</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RR tract</synonym_text>
</synonym>
<is_a>SO:0000186</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000436</id>
<name>ARS</name>
<def>
<defstr>A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>autonomously replicating sequence</synonym_text>
</synonym>
<is_a>SO:0000296</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000437</id>
<name>assortment_derived_duplication</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000438</id>
<name>gene_not_polyadenylated</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000439</id>
<name>inverted_ring_chromosome</name>
<synonym scope="exact">
<synonym_text>inverted ring chromosome</synonym_text>
</synonym>
<is_a>SO:1000030</is_a>
<is_a>SO:1000045</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000440</id>
<name>vector_replicon</name>
<def>
<defstr>A replicon that has been modified to act as a vector for foreign sequence.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>vector</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>vector replicon</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Vector_(molecular_biology)</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000151</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000441</id>
<name>ss_oligo</name>
<def>
<defstr>A single stranded oligonucleotide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>single strand oligo</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>single strand oligonucleotide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>single stranded oligonucleotide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ss oligo</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ss oligonucleotide</synonym_text>
</synonym>
<is_a>SO:0000696</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000442</id>
<name>ds_oligo</name>
<def>
<defstr>A double stranded oligonucleotide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>double stranded oligonucleotide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ds oligo</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ds-oligonucleotide</synonym_text>
</synonym>
<is_a>SO:0000696</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000443</id>
<name>polymer_attribute</name>
<def>
<defstr>An attribute to describe the kind of biological sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>polymer attribute</synonym_text>
</synonym>
<is_a>SO:0000400</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000444</id>
<name>three_prime_noncoding_exon</name>
<def>
<defstr>Non-coding exon in the 3' UTR.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>three prime noncoding exon</synonym_text>
</synonym>
<is_a>SO:0000198</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000445</id>
<name>five_prime_noncoding_exon</name>
<def>
<defstr>Non-coding exon in the 5' UTR.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5' nc exon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>5' non coding exon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime noncoding exon</synonym_text>
</synonym>
<is_a>SO:0000198</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000446</id>
<name>UTR_intron</name>
<def>
<defstr>Intron located in the untranslated region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>UTR intron</synonym_text>
</synonym>
<is_a>SO:0000188</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000447</id>
<name>five_prime_UTR_intron</name>
<def>
<defstr>An intron located in the 5' UTR.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>five prime UTR intron</synonym_text>
</synonym>
<is_a>SO:0000446</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000448</id>
<name>three_prime_UTR_intron</name>
<def>
<defstr>An intron located in the 3' UTR.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>three prime UTR intron</synonym_text>
</synonym>
<is_a>SO:0000446</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000449</id>
<name>random_sequence</name>
<def>
<defstr>A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>random sequence</synonym_text>
</synonym>
<is_a>SO:0000351</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000450</id>
<name>interband</name>
<def>
<defstr>A light region between two darkly staining bands in a polytene chromosome.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>chromosome interband</synonym_text>
</synonym>
<is_a>SO:0000830</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000451</id>
<name>gene_with_polyadenylated_mRNA</name>
<def>
<defstr>A gene that encodes a polyadenylated mRNA.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with polyadenylated mRNA</synonym_text>
</synonym>
<is_a>SO:0001217</is_a>
<intersection_of>
<to>SO:0001217</to>
</intersection_of>
<intersection_of>
<type>transcribed_to</type>
<to>SO:0000871</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000452</id>
<name>transgene_attribute</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000453</id>
<name>transposition</name>
<is_a>SO:1000183</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000454</id>
<name>rasiRNA</name>
<def>
<defstr>A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.</defstr>
<dbxref>
<acc>http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>repeat associated small interfering RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/RasiRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000455</id>
<name>gene_with_mRNA_with_frameshift</name>
<def>
<defstr>A gene that encodes an mRNA with a frameshift.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with mRNA with frameshift</synonym_text>
</synonym>
<is_a>SO:0001217</is_a>
<intersection_of>
<to>SO:0001217</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000865</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000456</id>
<name>recombinationally_rearranged_gene</name>
<def>
<defstr>A gene that is recombinationally rearranged.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>recombinationally rearranged gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000940</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000457</id>
<name>interchromosomal_duplication</name>
<def>
<defstr>A chromosome duplication involving an insertion from another chromosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>interchromosomal duplication</synonym_text>
</synonym>
<is_a>SO:1000037</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000458</id>
<name>D_gene</name>
<def>
<defstr>Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>D gene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>D-GENE</synonym_text>
</synonym>
<is_a>SO:0000460</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000459</id>
<name>gene_with_trans_spliced_transcript</name>
<def>
<defstr>A gene with a transcript that is trans-spliced.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with trans spliced transcript</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>transcribed_to</type>
<to>SO:0000479</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000460</id>
<name>vertebrate_immunoglobulin_T_cell_receptor_segment</name>
<comment>I am using the term segment instead of gene here to avoid confusion with the region 'gene'.</comment>
<synonym scope="exact">
<synonym_text>vertebrate immunoglobulin T cell receptor segment</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>vertebrate_immunoglobulin/T-cell receptor gene</synonym_text>
</synonym>
<is_a>SO:0000301</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000461</id>
<name>inversion_derived_bipartite_deficiency</name>
<def>
<defstr>A chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.</defstr>
<dbxref>
<acc>km</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>inversion derived bipartite deficiency</synonym_text>
</synonym>
<is_a>SO:1000029</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000462</id>
<name>pseudogenic_region</name>
<def>
<defstr>A non-functional descendent of a functional entity.</defstr>
<dbxref>
<acc>cjm</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>pseudogenic region</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000463</id>
<name>encodes_alternately_spliced_transcripts</name>
<def>
<defstr>A gene that encodes more than one transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>encodes alternately spliced transcripts</synonym_text>
</synonym>
<is_a>SO:0000401</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000464</id>
<name>decayed_exon</name>
<def>
<defstr>A non-functional descendant of an exon.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>decayed exon</synonym_text>
</synonym>
<is_a>SO:0000462</is_a>
<relationship>
<type>non_functional_homolog_of</type>
<to>SO:0000147</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000465</id>
<name>inversion_derived_deficiency_plus_duplication</name>
<def>
<defstr>A chromosome generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.</defstr>
<dbxref>
<acc>km</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>inversion derived deficiency plus duplication</synonym_text>
</synonym>
<is_a>SO:1000029</is_a>
<is_a>SO:1000038</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000466</id>
<name>V_gene</name>
<def>
<defstr>Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V gene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-GENE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>variable_gene</synonym_text>
</synonym>
<is_a>SO:0000460</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000467</id>
<name>post_translationally_regulated_by_protein_stability</name>
<def>
<defstr>An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>post translationally regulated by protein stability</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>post-translationally regulated by protein stability</synonym_text>
</synonym>
<is_a>SO:0000130</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000468</id>
<name>golden_path_fragment</name>
<def>
<defstr>One of the pieces of sequence that make up a golden path.</defstr>
<dbxref>
<acc>rd</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>golden path fragment</synonym_text>
</synonym>
<is_a>SO:0000143</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000688</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000469</id>
<name>post_translationally_regulated_by_protein_modification</name>
<def>
<defstr>An attribute describing a gene sequence where the resulting protein is modified to regulate it.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>post translationally regulated by protein modification</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>post-translationally regulated by protein modification</synonym_text>
</synonym>
<is_a>SO:0000130</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000470</id>
<name>J_gene</name>
<def>
<defstr>Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>J gene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>J-GENE</synonym_text>
</synonym>
<is_a>SO:0000460</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000471</id>
<name>autoregulated</name>
<def>
<defstr>The gene product is involved in its own transcriptional regulation.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000123</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000472</id>
<name>tiling_path</name>
<def>
<defstr>A set of regions which overlap with minimal polymorphism to form a linear sequence.</defstr>
<dbxref>
<acc>cjm</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>tiling path</synonym_text>
</synonym>
<is_a>SO:0000353</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000473</id>
<name>negatively_autoregulated</name>
<def>
<defstr>The gene product is involved in its own transcriptional regulation where it decreases transcription.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>negatively autoregulated</synonym_text>
</synonym>
<is_a>SO:0000126</is_a>
<is_a>SO:0000471</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000474</id>
<name>tiling_path_fragment</name>
<def>
<defstr>A piece of sequence that makes up a tiling_path (SO:0000472).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>tiling path fragment</synonym_text>
</synonym>
<is_a>SO:0000143</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000472</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000475</id>
<name>positively_autoregulated</name>
<def>
<defstr>The gene product is involved in its own transcriptional regulation, where it increases transcription.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>positively autoregulated</synonym_text>
</synonym>
<is_a>SO:0000125</is_a>
<is_a>SO:0000471</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000476</id>
<name>contig_read</name>
<def>
<defstr>A DNA sequencer read which is part of a contig.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>contig read</synonym_text>
</synonym>
<is_a>SO:0000150</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000477</id>
<name>polycistronic_gene</name>
<def>
<defstr>A gene that is polycistronic.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000478</id>
<name>C_gene</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205).</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>C gene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>C_GENE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>constant gene</synonym_text>
</synonym>
<is_a>SO:0000460</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000479</id>
<name>trans_spliced_transcript</name>
<def>
<defstr>A transcript that is trans-spliced.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>trans spliced transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>trans-spliced transcript</synonym_text>
</synonym>
<is_a>SO:0000673</is_a>
<intersection_of>
<to>SO:0000673</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000870</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000480</id>
<name>tiling_path_clone</name>
<def>
<defstr>A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>tiling path clone</synonym_text>
</synonym>
<is_a>SO:0000151</is_a>
<is_a>SO:0000474</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000481</id>
<name>terminal_inverted_repeat</name>
<def>
<defstr>An inverted repeat (SO:0000294) occuring at the termini of a DNA transposon.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>terminal inverted repeat</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>TIR</synonym_text>
</synonym>
<is_a>SO:0000294</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000208</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000482</id>
<name>vertebrate_immunoglobulin_T_cell_receptor_gene_cluster</name>
<synonym scope="exact">
<synonym_text>vertebrate immunoglobulin T cell receptor gene cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>vertebrate_immunoglobulin/T-cell receptor gene cluster</synonym_text>
</synonym>
<is_a>SO:0000301</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000483</id>
<name>nc_primary_transcript</name>
<def>
<defstr>A primary transcript that is never translated into a protein.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>nc primary transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>noncoding primary transcript</synonym_text>
</synonym>
<is_a>SO:0000185</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000484</id>
<name>three_prime_coding_exon_noncoding_region</name>
<def>
<defstr>The sequence of the 3' exon that is not coding.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>three prime coding exon noncoding region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three_prime_exon_noncoding_region</synonym_text>
</synonym>
<is_a>SO:0001214</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000202</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000485</id>
<name>DJ_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>(DJ)-J-CLUSTER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DJ J cluster</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000486</id>
<name>five_prime_coding_exon_noncoding_region</name>
<def>
<defstr>The sequence of the 5' exon preceding the start codon.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>five prime coding exon noncoding region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five_prime_exon_noncoding_region</synonym_text>
</synonym>
<is_a>SO:0001214</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000200</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000487</id>
<name>VDJ_J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>(VDJ)-J-C-CLUSTER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>VDJ J C cluster</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000574</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000488</id>
<name>VDJ_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>(VDJ)-J-CLUSTER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>VDJ J cluster</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000574</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000489</id>
<name>VJ_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(VJ)-C-CLUSTER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>VJ C cluster</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000576</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000490</id>
<name>VJ_J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>(VJ)-J-C-CLUSTER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>VJ J C cluster</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000576</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000491</id>
<name>VJ_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>(VJ)-J-CLUSTER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>VJ J cluster</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000576</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000492</id>
<name>D_gene_recombination_feature</name>
<synonym scope="exact">
<synonym_text>D gene recombination feature</synonym_text>
</synonym>
<is_a>SO:0000939</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000493</id>
<name>three_prime_D_heptamer</name>
<def>
<defstr>7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3'D-HEPTAMER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime D heptamer</synonym_text>
</synonym>
<is_a>SO:0000561</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000570</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000494</id>
<name>three_prime_D_nonamer</name>
<def>
<defstr>A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3'D-NOMAMER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime D nonamer</synonym_text>
</synonym>
<is_a>SO:0000562</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000570</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000495</id>
<name>three_prime_D_spacer</name>
<def>
<defstr>A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3'D-SPACER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime D spacer</synonym_text>
</synonym>
<is_a>SO:0000563</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000570</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000496</id>
<name>five_prime_D_heptamer</name>
<def>
<defstr>7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5'D-HEPTAMER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime D heptamer</synonym_text>
</synonym>
<is_a>SO:0000561</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000556</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000497</id>
<name>five_prime_D_nonamer</name>
<def>
<defstr>9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5'D-NONAMER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime D nonamer</synonym_text>
</synonym>
<is_a>SO:0000562</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000556</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000498</id>
<name>five_prime_D_spacer</name>
<def>
<defstr>12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5'-SPACER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime D spacer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime D-spacer</synonym_text>
</synonym>
<is_a>SO:0000563</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000556</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000499</id>
<name>virtual_sequence</name>
<def>
<defstr>A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>virtual sequence</synonym_text>
</synonym>
<is_a>SO:0000353</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000500</id>
<name>Hoogsteen_base_pair</name>
<def>
<defstr>A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds.</defstr>
<dbxref>
<acc>12177293</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>Hoogsteen base pair</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Hoogsteen_base_pair</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000028</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000501</id>
<name>reverse_Hoogsteen_base_pair</name>
<def>
<defstr>A type of non-canonical base-pairing.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>reverse Hoogsteen base pair</synonym_text>
</synonym>
<is_a>SO:0000028</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000502</id>
<name>transcribed_region</name>
<def>
<defstr>A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.</comment>
<subset>SOFA</subset>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000503</id>
<name>alternately_spliced_gene_encodeing_one_transcript</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000504</id>
<name>D_DJ_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>D DJ C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>D-(DJ)-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000505</id>
<name>D_DJ_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>D DJ cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>D-(DJ)-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000506</id>
<name>D_DJ_J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>D DJ J C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>D-(DJ)-J-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000507</id>
<name>pseudogenic_exon</name>
<def>
<defstr>A non functional descendant of an exon, part of a pseudogene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutatations.</comment>
<synonym scope="exact">
<synonym_text>pseudogenic exon</synonym_text>
</synonym>
<is_a>SO:0000462</is_a>
<relationship>
<type>non_functional_homolog_of</type>
<to>SO:0000147</to>
</relationship>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000516</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000508</id>
<name>D_DJ_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>D DJ J cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>D-(DJ)-J-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000509</id>
<name>D_J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>D J C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>D-J-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000482</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000510</id>
<name>VD_gene</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205).</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V_D_GENE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>VD gene</synonym_text>
</synonym>
<is_a>SO:0000936</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000511</id>
<name>J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>J C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>J-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000482</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000512</id>
<name>inversion_derived_deficiency_plus_aneuploid</name>
<def>
<defstr>A chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion.</defstr>
<dbxref>
<acc>km</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>inversion derived deficiency plus aneuploid</synonym_text>
</synonym>
<is_a>SO:1000029</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000513</id>
<name>J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>J cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>J-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000482</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000514</id>
<name>J_nonamer</name>
<def>
<defstr>9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>J nonamer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>J-NONAMER</synonym_text>
</synonym>
<is_a>SO:0000562</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000302</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000515</id>
<name>J_heptamer</name>
<def>
<defstr>7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>J heptamer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>J-HEPTAMER</synonym_text>
</synonym>
<is_a>SO:0000561</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000302</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000516</id>
<name>pseudogenic_transcript</name>
<def>
<defstr>A non functional descendant of a transcript, part of a pseudogene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutatations.</comment>
<synonym scope="exact">
<synonym_text>pseudogenic transcript</synonym_text>
</synonym>
<is_a>SO:0000462</is_a>
<relationship>
<type>non_functional_homolog_of</type>
<to>SO:0000673</to>
</relationship>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000336</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000517</id>
<name>J_spacer</name>
<def>
<defstr>12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>J spacer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>J-SPACER</synonym_text>
</synonym>
<is_a>SO:0000563</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000302</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000518</id>
<name>V_DJ_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V DJ cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-(DJ)-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000519</id>
<name>V_DJ_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V DJ J cluster</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>V-(DJ)-J-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000520</id>
<name>V_VDJ_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V VDJ C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-(VDJ)-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000574</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000521</id>
<name>V_VDJ_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V VDJ cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-(VDJ)-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000574</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000522</id>
<name>V_VDJ_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V VDJ J cluster</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>V-(VDJ)-J-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000574</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000523</id>
<name>V_VJ_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V VJ C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-(VJ)-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000576</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000524</id>
<name>V_VJ_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V VJ cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-(VJ)-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000576</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000525</id>
<name>V_VJ_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V VJ J cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-(VJ)-J-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000576</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000526</id>
<name>V_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000482</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000527</id>
<name>V_D_DJ_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V D DJ C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-D-(DJ)-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000528</id>
<name>V_D_DJ_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V D DJ cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-D-(DJ)-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000529</id>
<name>V_D_DJ_J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V D DJ J C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-D-(DJ)-J-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000530</id>
<name>V_D_DJ_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V D DJ J cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-D-(DJ)-J-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000531</id>
<name>V_D_J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V D J C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-D-J-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000532</id>
<name>V_D_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V D J cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-D-J-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000533</id>
<name>V_heptamer</name>
<def>
<defstr>7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V heptamer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-HEPTAMER</synonym_text>
</synonym>
<is_a>SO:0000561</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000538</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000534</id>
<name>V_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V J cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-J-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000482</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000535</id>
<name>V_J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V J C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-J-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000482</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000536</id>
<name>V_nonamer</name>
<def>
<defstr>9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V nonamer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-NONAMER</synonym_text>
</synonym>
<is_a>SO:0000562</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000538</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000537</id>
<name>V_spacer</name>
<def>
<defstr>12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V spacer</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-SPACER</synonym_text>
</synonym>
<is_a>SO:0000563</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000538</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000538</id>
<name>V_gene_recombination_feature</name>
<def>
<defstr>Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V gene recombination feature</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-RS</synonym_text>
</synonym>
<is_a>SO:0000939</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000539</id>
<name>DJ_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>(DJ)-C-CLUSTER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DJ C cluster</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000540</id>
<name>DJ_J_C_cluster</name>
<def>
<defstr>Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>(DJ)-J-C-CLUSTER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DJ J C cluster</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000541</id>
<name>VDJ_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>(VDJ)-C-CLUSTER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>VDJ C cluster</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000574</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000542</id>
<name>V_DJ_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V DJ C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-(DJ)-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000543</id>
<name>alternately_spliced_gene_encoding_greater_than_one_transcript</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000544</id>
<name>helitron</name>
<def>
<defstr>A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons.</defstr>
<dbxref>
<acc>http://www.pnas.org/cgi/content/full/100/11/6569</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>ISCR</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Helitron</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000182</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000545</id>
<name>recoding_pseudoknot</name>
<def>
<defstr>The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding.</defstr>
<dbxref>
<acc>http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>recoding pseudoknot</synonym_text>
</synonym>
<is_a>SO:0000591</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:1001268</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000546</id>
<name>designed_sequence</name>
<synonym scope="exact">
<synonym_text>designed sequence</synonym_text>
</synonym>
<is_a>SO:0000351</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000547</id>
<name>inversion_derived_bipartite_duplication</name>
<def>
<defstr>A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion.</defstr>
<dbxref>
<acc>km</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>inversion derived bipartite duplication</synonym_text>
</synonym>
<is_a>SO:1000038</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000548</id>
<name>gene_with_edited_transcript</name>
<def>
<defstr>A gene that encodes a transcript that is edited.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with edited transcript</synonym_text>
</synonym>
<is_a>SO:0001217</is_a>
<intersection_of>
<to>SO:0001217</to>
</intersection_of>
<intersection_of>
<type>transcribed_to</type>
<to>SO:0000873</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000549</id>
<name>inversion_derived_duplication_plus_aneuploid</name>
<def>
<defstr>A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion.</defstr>
<dbxref>
<acc>km</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>inversion derived duplication plus aneuploid</synonym_text>
</synonym>
<is_a>SO:1000038</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000550</id>
<name>aneuploid_chromosome</name>
<synonym scope="exact">
<synonym_text>aneuploid chromosome</synonym_text>
</synonym>
<is_a>SO:1000183</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000551</id>
<name>polyA_signal_sequence</name>
<def>
<defstr>The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>poly(A) signal</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polyA signal sequence</synonym_text>
</synonym>
<is_a>SO:0005836</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000552</id>
<name>Shine_Dalgarno_sequence</name>
<def>
<defstr>Region in 5' UTR where ribosome assembles on mRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>five prime ribosome binding site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>RBS</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Shine Dalgarno sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Shine-Dalgarno sequence</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000139</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000553</id>
<name>polyA_site</name>
<def>
<defstr>The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>polyA site</synonym_text>
</synonym>
<is_a>SO:0000837</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000205</to>
</relationship>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000233</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000554</id>
<name>assortment_derived_deficiency_plus_duplication</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000555</id>
<name>five_prime_clip</name>
<def>
<defstr>5' most region of a precursor transcript that is clipped off during processing.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>5' clip</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime clip</synonym_text>
</synonym>
<is_a>SO:0000303</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000556</id>
<name>five_prime_D_recombination_signal_sequence</name>
<def>
<defstr>Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5'RS</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime D recombination signal sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime D-recombination signal sequence</synonym_text>
</synonym>
<is_a>SO:0000492</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000557</id>
<name>three_prime_clip</name>
<def>
<defstr>3'-most region of a precursor transcript that is clipped off during processing.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3'-clip</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime clip</synonym_text>
</synonym>
<is_a>SO:0000303</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000558</id>
<name>C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/ligmb/LIGMlect?query=7</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000482</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000559</id>
<name>D_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>D cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>D-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000482</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000560</id>
<name>D_J_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>D J cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>D-J-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000482</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000458</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000561</id>
<name>heptamer_of_recombination_feature_of_vertebrate_immune_system_gene</name>
<def>
<defstr>Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>HEPTAMER</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>heptamer of recombination feature of vertebrate immune system gene</synonym_text>
</synonym>
<is_a>SO:0000939</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000562</id>
<name>nonamer_of_recombination_feature_of_vertebrate_immune_system_gene</name>
<synonym scope="exact">
<synonym_text>nonamer of recombination feature of vertebrate immune system gene</synonym_text>
</synonym>
<is_a>SO:0000939</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000563</id>
<name>vertebrate_immune_system_gene_recombination_spacer</name>
<synonym scope="exact">
<synonym_text>vertebrate immune system gene recombination spacer</synonym_text>
</synonym>
<is_a>SO:0000301</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000564</id>
<name>V_DJ_J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V DJ J C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-(DJ)-J-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000572</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000565</id>
<name>V_VDJ_J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V VDJ J C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-(VDJ)-J-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000574</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000566</id>
<name>V_VJ_J_C_cluster</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V VJ J C cluster</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>V-(VJ)-J-C-CLUSTER</synonym_text>
</synonym>
<is_a>SO:0000938</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000466</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000470</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000478</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0000576</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000567</id>
<name>inversion_derived_aneuploid_chromosome</name>
<def>
<defstr>A chromosome may be generated by recombination between two inverversions; presumed to have a deficiency or duplication at each end of the inversion.</defstr>
<dbxref>
<acc>km</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>inversion derived aneuploid chromosome</synonym_text>
</synonym>
<is_a>SO:0000550</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000568</id>
<name>bidirectional_promoter</name>
<synonym scope="exact">
<synonym_text>bidirectional promoter</synonym_text>
</synonym>
<is_a>SO:0000167</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000569</id>
<name>retrotransposed</name>
<alt_id>SO:0100042</alt_id>
<def>
<defstr>An attribute of a feature that occured as the product of a reverse transcriptase mediated event.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>GO:0003964 RNA-directed DNA polymerase activity.</comment>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Retrotransposed</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000570</id>
<name>three_prime_D_recombination_signal_sequence</name>
<def>
<defstr>Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3'D-RS</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime D recombination signal sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three_prime_D-recombination_signal_sequence</synonym_text>
</synonym>
<is_a>SO:0000492</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000571</id>
<name>miRNA_encoding</name>
<synonym scope="exact">
<synonym_text>miRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000572</id>
<name>DJ_gene</name>
<def>
<defstr>Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment.</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>D-J-GENE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DJ gene</synonym_text>
</synonym>
<is_a>SO:0000936</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000573</id>
<name>rRNA_encoding</name>
<synonym scope="exact">
<synonym_text>rRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000574</id>
<name>VDJ_gene</name>
<def>
<defstr>Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V-D-J-GENE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>VDJ gene</synonym_text>
</synonym>
<is_a>SO:0000936</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000575</id>
<name>scRNA_encoding</name>
<synonym scope="exact">
<synonym_text>scRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000576</id>
<name>VJ_gene</name>
<def>
<defstr>Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).</defstr>
<dbxref>
<acc>http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>V-J-GENE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>VJ gene</synonym_text>
</synonym>
<is_a>SO:0000936</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000577</id>
<name>centromere</name>
<def>
<defstr>A region of chromosome where the spindle fibers attach during mitosis and meiosis.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Centromere</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000628</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000578</id>
<name>snoRNA_encoding</name>
<synonym scope="exact">
<synonym_text>snoRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000579</id>
<name>edited_transcript_feature</name>
<def>
<defstr>A locatable feature on a transcript that is edited.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>edited transcript feature</synonym_text>
</synonym>
<is_a>SO:0000833</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000580</id>
<name>methylation_guide_snoRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a methylation guide small nucleolar RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>methylation guide snoRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000232</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000581</id>
<name>cap</name>
<def>
<defstr>A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.</defstr>
<dbxref>
<acc>http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/5%27_cap</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000582</id>
<name>rRNA_cleavage_snoRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding an rRNA cleavage snoRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>rRNA cleavage snoRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000232</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000583</id>
<name>pre_edited_region</name>
<def>
<defstr>The region of a transcript that will be edited.</defstr>
<dbxref>
<acc>http://dna.kdna.ucla.edu/rna/index.aspx</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>pre edited region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>pre-edited region</synonym_text>
</synonym>
<is_a>SO:0000579</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000584</id>
<name>tmRNA</name>
<def>
<defstr>A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and eukaryote nuclear genomes.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>10Sa RNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>ssrA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/TmRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000370</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000585</id>
<name>C_D_box_snoRNA_encoding</name>
<synonym scope="exact">
<synonym_text>C/D box snoRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000578</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000586</id>
<name>tmRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a tmRNA (SO:0000584).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>10Sa RNA primary transcript</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>ssrA RNA primary transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>tmRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000587</id>
<name>group_I_intron</name>
<def>
<defstr>Group I catalytic introns are large self-splicing ribozymes. They catalyse their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>GO:0000372.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>group I intron</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Group_I_intron</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000588</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000588</id>
<name>autocatalytically_spliced_intron</name>
<def>
<defstr>A self spliced intron.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>autocatalytically spliced intron</synonym_text>
</synonym>
<is_a>SO:0000188</is_a>
<intersection_of>
<to>SO:0000188</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001186</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000589</id>
<name>SRP_RNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a signal recognition particle RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>SRP RNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000590</id>
<name>SRP_RNA</name>
<def>
<defstr>The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>7S RNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>signal recognition particle RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>SRP RNA</synonym_text>
</synonym>
<is_a>SO:0000655</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000589</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000591</id>
<name>pseudoknot</name>
<def>
<defstr>A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Pseudoknot</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000592</id>
<name>H_pseudoknot</name>
<def>
<defstr>A pseudoknot which contains two stems and at least two loops.</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>classical pseudoknot</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>H pseudoknot</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>H-pseudoknot</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>H-type pseudoknot</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>hairpin-type pseudoknot</synonym_text>
</synonym>
<is_a>SO:0000591</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000593</id>
<name>C_D_box_snoRNA</name>
<def>
<defstr>Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.</defstr>
<dbxref>
<acc>http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>box C/D snoRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>C D box snoRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>C/D box snoRNA</synonym_text>
</synonym>
<is_a>SO:0000275</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000595</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000594</id>
<name>H_ACA_box_snoRNA</name>
<def>
<defstr>Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.</defstr>
<dbxref>
<acc>http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>box H/ACA snoRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>H ACA box snoRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>H/ACA box snoRNA</synonym_text>
</synonym>
<is_a>SO:0000275</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000596</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000595</id>
<name>C_D_box_snoRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a small nucleolar RNA of the box C/D family.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>C/D box snoRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000232</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000596</id>
<name>H_ACA_box_snoRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a small nucleolar RNA of the box H/ACA family.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>H ACA box snoRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000232</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000597</id>
<name>transcript_edited_by_U_insertion/deletion</name>
<def>
<defstr>The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.</defstr>
<dbxref>
<acc>http://www.rna.ucla.edu/index.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000598</id>
<name>edited_by_C_insertion_and_dinucleotide_insertion</name>
<synonym scope="related">
<synonym_text>transcript_edited_by_C-insertion_and_dinucleotide_insertion</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000599</id>
<name>edited_by_C_to_U_substitution</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000600</id>
<name>edited_by_A_to_I_substitution</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000601</id>
<name>edited_by_G_addition</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000602</id>
<name>guide_RNA</name>
<def>
<defstr>A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.</defstr>
<dbxref>
<acc>http://www.rna.ucla.edu/index.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>gRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>guide RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Guide_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000603</id>
<name>group_II_intron</name>
<def>
<defstr>Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>GO:0000373.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>group II intron</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Group_II_intron</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000588</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000604</id>
<name>editing_block</name>
<def>
<defstr>Edited mRNA sequence mediated by a single guide RNA (SO:0000602).</defstr>
<dbxref>
<acc>http://dna.kdna.ucla.edu/rna/index.aspx</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>editing block</synonym_text>
</synonym>
<is_a>SO:0000579</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000605</id>
<name>intergenic_region</name>
<def>
<defstr>A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.</defstr>
<dbxref>
<acc>cjm</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>intergenic region</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Intergenic_region</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000606</id>
<name>editing_domain</name>
<def>
<defstr>Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).</defstr>
<dbxref>
<acc>http://dna.kdna.ucla.edu/rna/index.aspx</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>editing domain</synonym_text>
</synonym>
<is_a>SO:0000579</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000607</id>
<name>unedited_region</name>
<def>
<defstr>The region of an edited transcript that will not be edited.</defstr>
<dbxref>
<acc>http://dna.kdna.ucla.edu/rna/index.aspx</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>unedited region</synonym_text>
</synonym>
<is_a>SO:0000579</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000608</id>
<name>H_ACA_box_snoRNA_encoding</name>
<synonym scope="exact">
<synonym_text>H ACA box snoRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000578</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000609</id>
<name>oligo_U_tail</name>
<def>
<defstr>The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).</defstr>
<dbxref>
<acc>http://www.rna.ucla.edu/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>oligo U tail</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<relationship>
<type>adjacent_to</type>
<to>SO:0000602</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000610</id>
<name>polyA_sequence</name>
<def>
<defstr>Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>polyA sequence</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<relationship>
<type>adjacent_to</type>
<to>SO:0000234</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000611</id>
<name>branch_site</name>
<def>
<defstr>A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>branch point</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>branch site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>branch_point</synonym_text>
</synonym>
<is_a>SO:0000841</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000612</id>
<name>polypyrimidine_tract</name>
<def>
<defstr>The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.</defstr>
<dbxref>
<acc>http://nar.oupjournals.org/cgi/content/full/25/4/888</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>polypyrimidine tract</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Polypyrimidine_tract</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000841</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000613</id>
<name>bacterial_RNApol_promoter</name>
<def>
<defstr>A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>bacterial RNApol promoter</synonym_text>
</synonym>
<is_a>SO:0000752</is_a>
<is_a>SO:0001203</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000614</id>
<name>bacterial_terminator</name>
<def>
<defstr>A terminator signal for bacterial transcription.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>bacterial terminator</synonym_text>
</synonym>
<is_a>SO:0000141</is_a>
<is_a>SO:0000752</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000615</id>
<name>terminator_of_type_2_RNApol_III_promoter</name>
<def>
<defstr>A terminator signal for RNA polymerase III transcription.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>terminator of type 2 RNApol III promoter</synonym_text>
</synonym>
<is_a>SO:0000951</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000616</id>
<name>transcription_end_site</name>
<def>
<defstr>The base where transcription ends.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>transcription end site</synonym_text>
</synonym>
<is_a>SO:0000835</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000617</id>
<name>RNApol_III_promoter_type_1</name>
<synonym scope="exact">
<synonym_text>RNApol III promoter type 1</synonym_text>
</synonym>
<is_a>SO:0000171</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000618</id>
<name>RNApol_III_promoter_type_2</name>
<synonym scope="exact">
<synonym_text>RNApol III promoter type 2</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>tRNA promoter</synonym_text>
</synonym>
<is_a>SO:0000171</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000619</id>
<name>A_box</name>
<def>
<defstr>A variably distant linear promoter region recognised by TFIIIC, with consensus sequence TGGCnnAGTGG.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>A-box</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/A-box</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000618</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000620</id>
<name>B_box</name>
<def>
<defstr>A variably distant linear promoter region recognised by TFIIIC, with consensus sequence AGGTTCCAnnCC.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>B-box</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000618</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000621</id>
<name>RNApol_III_promoter_type_3</name>
<synonym scope="exact">
<synonym_text>RNApol III promoter type 3</synonym_text>
</synonym>
<is_a>SO:0000171</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000622</id>
<name>C_box</name>
<def>
<defstr>An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>C-box</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000617</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000623</id>
<name>snRNA_encoding</name>
<synonym scope="exact">
<synonym_text>snRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000624</id>
<name>telomere</name>
<def>
<defstr>A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>telomeric DNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>telomeric sequence</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Telomere</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000628</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000625</id>
<name>silencer</name>
<def>
<defstr>A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Silencer_(DNA)</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000727</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000626</id>
<name>chromosomal_regulatory_element</name>
<synonym scope="exact">
<synonym_text>chromosomal regulatory element</synonym_text>
</synonym>
<is_a>SO:0000830</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000627</id>
<name>insulator</name>
<def>
<defstr>A trancriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.</defstr>
<dbxref>
<acc>regcreative</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>insulator element</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Insulator_(genetics)</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001055</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000628</id>
<name>chromosomal_structural_element</name>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>chromosomal structural element</synonym_text>
</synonym>
<is_a>SO:0000830</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000629</id>
<name>five_prime_open_reading_frame</name>
<synonym scope="exact">
<synonym_text>five prime open reading frame</synonym_text>
</synonym>
<is_a>SO:0000836</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000204</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000630</id>
<name>upstream_AUG_codon</name>
<def>
<defstr>A start codon upstream of the ORF.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>upstream AUG codon</synonym_text>
</synonym>
<is_a>SO:0000837</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000203</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000631</id>
<name>polycistronic_primary_transcript</name>
<def>
<defstr>A primary transcript encoding for more than one gene product.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>polycistronic primary transcript</synonym_text>
</synonym>
<is_a>SO:0000078</is_a>
<is_a>SO:0000185</is_a>
<intersection_of>
<to>SO:0000185</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000880</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000632</id>
<name>monocistronic_primary_transcript</name>
<def>
<defstr>A primary transcript encoding for one gene product.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>monocistronic primary transcript</synonym_text>
</synonym>
<is_a>SO:0000185</is_a>
<is_a>SO:0000665</is_a>
<intersection_of>
<to>SO:0000185</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000878</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000633</id>
<name>monocistronic_mRNA</name>
<def>
<defstr>An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.</defstr>
<dbxref>
<acc>rd</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>monocistronic mRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>monocistronic processed transcript</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Monocistronic_mRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000234</is_a>
<is_a>SO:0000665</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000878</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000634</id>
<name>polycistronic_mRNA</name>
<def>
<defstr>An mRNA that encodes multiple proteins from at least two non-overlapping regions.</defstr>
<dbxref>
<acc>rd</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>polycistronic mRNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>polycistronic processed transcript</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Polycistronic_mRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000078</is_a>
<is_a>SO:0000234</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000880</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000635</id>
<name>mini_exon_donor_RNA</name>
<def>
<defstr>A primary transcript that donates the spliced leader to other mRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mini exon donor RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>mini-exon donor RNA</synonym_text>
</synonym>
<is_a>SO:0000185</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000636</id>
<name>spliced_leader_RNA</name>
<synonym scope="related">
<synonym_text>mini-exon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>spliced leader RNA</synonym_text>
</synonym>
<is_a>SO:0000835</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000635</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000637</id>
<name>engineered_plasmid</name>
<def>
<defstr>A plasmid that is engineered.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered plasmid</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>engineered plasmid gene</synonym_text>
</synonym>
<is_a>SO:0000155</is_a>
<is_a>SO:0000804</is_a>
<intersection_of>
<to>SO:0000155</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000638</id>
<name>transcribed_spacer_region</name>
<def>
<defstr>Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.</defstr>
<dbxref>
<acc>http://oregonstate.edu/instruction/bb492/general/glossary.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>transcribed spacer region</synonym_text>
</synonym>
<is_a>SO:0000838</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000639</id>
<name>internal_transcribed_spacer_region</name>
<def>
<defstr>Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>internal transcribed spacer region</synonym_text>
</synonym>
<is_a>SO:0000638</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000640</id>
<name>external_transcribed_spacer_region</name>
<def>
<defstr>Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>external transcribed spacer region</synonym_text>
</synonym>
<is_a>SO:0000638</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000641</id>
<name>tetranucleotide_repeat_microsatellite_feature</name>
<synonym scope="exact">
<synonym_text>tetranucleotide repeat microsatellite feature</synonym_text>
</synonym>
<is_a>SO:0000289</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000642</id>
<name>SRP_RNA_encoding</name>
<synonym scope="exact">
<synonym_text>SRP RNA encoding</synonym_text>
</synonym>
<is_a>SO:0000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000643</id>
<name>minisatellite</name>
<def>
<defstr>A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.</defstr>
<dbxref>
<acc>http://www.informatics.jax.org/silver/glossary.shtml</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Minisatellite</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000005</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000644</id>
<name>antisense_RNA</name>
<def>
<defstr>Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>antisense RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Antisense_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000645</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000645</id>
<name>antisense_primary_transcript</name>
<def>
<defstr>The reverse complement of the primary transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>antisense primary transcript</synonym_text>
</synonym>
<is_a>SO:0000185</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000646</id>
<name>siRNA</name>
<def>
<defstr>A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.</defstr>
<dbxref>
<acc>12592000</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small interfering RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/SiRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000647</id>
<name>miRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a micro RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>micro RNA primary transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>miRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000648</id>
<name>stRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding a small temporal mRNA (SO:0000649).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>small temporal RNA primary transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>stRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000647</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000649</id>
<name>stRNA</name>
<def>
<defstr>Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans.</defstr>
<dbxref>
<acc>11081512</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small temporal RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/StRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000650</id>
<name>small_subunit_rRNA</name>
<def>
<defstr>Ribosomal RNA transcript that structures the small subunit of the ribosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>small subunit rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>SSU RNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>SSU rRNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<is_a>SO:0000252</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000255</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000651</id>
<name>large_subunit_rRNA</name>
<def>
<defstr>Ribosomal RNA transcript that structures the large subunit of the ribosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>large subunit rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>LSU RNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>LSU rRNA</synonym_text>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</synonym>
<is_a>SO:0000252</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000325</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000652</id>
<name>rRNA_5S</name>
<def>
<defstr>5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilises 5S rRNA until it is required for transcription.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>5S LSU rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>5S ribosomal RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>5S rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rRNA 5S</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/5S_ribosomal_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000651</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000653</id>
<name>rRNA_28S</name>
<def>
<defstr>A component of the large ribosomal subunit.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>28S LSU rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>28S ribosomal RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>28S rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rRNA 28S</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/28S_ribosomal_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000651</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000654</id>
<name>maxicircle_gene</name>
<def>
<defstr>A mitochondrial gene located in a maxicircle.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>maxi-circle gene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>maxicircle gene</synonym_text>
</synonym>
<is_a>SO:0000089</is_a>
<intersection_of>
<to>SO:0000089</to>
</intersection_of>
<intersection_of>
<type>OBO_REL:part_of</type>
<to>SO:0000742</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000655</id>
<name>ncRNA</name>
<def>
<defstr>An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>noncoding RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/NcRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000233</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000656</id>
<name>stRNA_encoding</name>
<synonym scope="exact">
<synonym_text>stRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000657</id>
<name>repeat_region</name>
<def>
<defstr>A region of sequence containing one or more repeat units.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>repeat region</synonym_text>
</synonym>
<is_a>SO:0001412</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000726</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000658</id>
<name>dispersed_repeat</name>
<def>
<defstr>A repeat that is located at dispersed sites in the genome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>dispersed repeat</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>interspersed repeat</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Interspersed_repeat</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000657</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000659</id>
<name>tmRNA_encoding</name>
<synonym scope="exact">
<synonym_text>tmRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000660</id>
<name>DNA_invertase_target_sequence</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000661</id>
<name>intron_attribute</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000662</id>
<name>spliceosomal_intron</name>
<def>
<defstr>An intron which is spliced by the spliceosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>GO:0000398.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>spliceosomal intron</synonym_text>
</synonym>
<is_a>SO:0000188</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000663</id>
<name>tRNA_encoding</name>
<synonym scope="exact">
<synonym_text>tRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000664</id>
<name>introgressed_chromosome_region</name>
<synonym scope="exact">
<synonym_text>introgressed chromosome region</synonym_text>
</synonym>
<is_a>SO:0000830</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000665</id>
<name>monocistronic_transcript</name>
<def>
<defstr>A transcript that is monocistronic.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>monocistronic transcript</synonym_text>
</synonym>
<is_a>SO:0000673</is_a>
<intersection_of>
<to>SO:0000673</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000878</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000666</id>
<name>mobile_intron</name>
<def>
<defstr>An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mobile intron</synonym_text>
</synonym>
<is_a>SO:0000188</is_a>
<is_a>SO:0001037</is_a>
<intersection_of>
<to>SO:0000188</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001234</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000667</id>
<name>insertion</name>
<alt_id>SO:1000034</alt_id>
<def>
<defstr>The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>nucleotide insertion</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nucleotide_insertion</synonym_text>
</synonym>
<is_a>SO:0001059</is_a>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000668</id>
<name>EST_match</name>
<def>
<defstr>A match against an EST sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>EST match</synonym_text>
</synonym>
<is_a>SO:0000102</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000669</id>
<name>sequence_rearrangement_feature</name>
<synonym scope="exact">
<synonym_text>sequence rearrangement feature</synonym_text>
</synonym>
<is_a>SO:0000298</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000670</id>
<name>chromosome_breakage_sequence</name>
<def>
<defstr>A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>chromosome breakage sequence</synonym_text>
</synonym>
<is_a>SO:0000669</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000671</id>
<name>internal_eliminated_sequence</name>
<def>
<defstr>A sequence eliminated from the genome of ciliates during nuclear differentiation.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>internal eliminated sequence</synonym_text>
</synonym>
<is_a>SO:0000669</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000672</id>
<name>macronucleus_destined_segment</name>
<def>
<defstr>A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>macronucleus destined segment</synonym_text>
</synonym>
<is_a>SO:0000669</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000673</id>
<name>transcript</name>
<def>
<defstr>An RNA synthesized on a DNA or RNA template by an RNA polymerase.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000831</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000674</id>
<name>non_canonical_splice_site</name>
<def>
<defstr>A splice site where the donor and acceptor sites differ from the canonical form.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>non canonical splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non-canonical splice site</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<consider>SO:0000678</consider>
<consider>SO:0000679</consider>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000675</id>
<name>canonical_splice_site</name>
<def>
<defstr>The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>canonical splice site</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<consider>SO:0000676</consider>
<consider>SO:0000677</consider>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000676</id>
<name>canonical_three_prime_splice_site</name>
<def>
<defstr>The canonical 3' splice site has the sequence "AG".</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>canonical 3' splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>canonical three prime splice site</synonym_text>
</synonym>
<is_a>SO:0000164</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000677</id>
<name>canonical_five_prime_splice_site</name>
<def>
<defstr>The canonical 5' splice site has the sequence "GT".</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>canonical 5' splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>canonical five prime splice site</synonym_text>
</synonym>
<is_a>SO:0000163</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000678</id>
<name>non_canonical_three_prime_splice_site</name>
<def>
<defstr>A 3' splice site that does not have the sequence "AG".</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>non canonical 3' splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non canonical three prime splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non-canonical three prime splice site</synonym_text>
</synonym>
<is_a>SO:0000164</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000679</id>
<name>non_canonical_five_prime_splice_site</name>
<def>
<defstr>A 5' splice site which does not have the sequence "GT".</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>non canonical 5' splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non canonical five prime splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non-canonical five prime splice site</synonym_text>
</synonym>
<is_a>SO:0000163</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000680</id>
<name>non_canonical_start_codon</name>
<def>
<defstr>A start codon that is not the usual AUG sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>non ATG start codon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non canonical start codon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non-canonical start codon</synonym_text>
</synonym>
<is_a>SO:0000318</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000681</id>
<name>aberrant_processed_transcript</name>
<def>
<defstr>A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>aberrant processed transcript</synonym_text>
</synonym>
<is_a>SO:0000673</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000682</id>
<name>splicing_feature</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000683</id>
<name>exonic_splice_enhancer</name>
<def>
<defstr>Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>exonic splice enhancer</synonym_text>
</synonym>
<is_a>SO:0000344</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000684</id>
<name>nuclease_sensitive_site</name>
<def>
<defstr>A region of nucleotide sequence targeted by a nuclease enzyme.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>nuclease sensitive site</synonym_text>
</synonym>
<is_a>SO:0000059</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000685</id>
<name>DNAseI_hypersensitive_site</name>
<synonym scope="exact">
<synonym_text>DHS</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DNAseI hypersensitive site</synonym_text>
</synonym>
<is_a>SO:0000322</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000686</id>
<name>translocation_element</name>
<def>
<defstr>For some translocations, particularly but not exclusively, reciprocal translocations, the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>translocation element</synonym_text>
</synonym>
<is_a>SO:1000044</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000687</id>
<name>deletion_junction</name>
<def>
<defstr>The space between two bases in a sequence which marks the position where a deletion has occurred.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>deletion junction</synonym_text>
</synonym>
<is_a>SO:0000699</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000688</id>
<name>golden_path</name>
<def>
<defstr>A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.</defstr>
<dbxref>
<acc>ls</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>golden path</synonym_text>
</synonym>
<is_a>SO:0000353</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000689</id>
<name>cDNA_match</name>
<def>
<defstr>A match against cDNA sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>cDNA match</synonym_text>
</synonym>
<is_a>SO:0000102</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000690</id>
<name>gene_with_polycistronic_transcript</name>
<def>
<defstr>A gene that encodes a polycistronic transcript.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with polycistronic transcript</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>transcribed_to</type>
<to>SO:0000078</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000691</id>
<name>cleaved_initiator_methionine</name>
<alt_id>BS:00067</alt_id>
<def>
<defstr>The initiator methionine that has been cleaved from a mature polypeptide sequence.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>cleaved initiator methionine</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>init_met</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="related">
<synonym_text>initiator methionine</synonym_text>
</synonym>
<is_a>SO:0100011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000692</id>
<name>gene_with_dicistronic_transcript</name>
<def>
<defstr>A gene that encodes a dicistronic transcript.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with dicistronic transcript</synonym_text>
</synonym>
<is_a>SO:0000690</is_a>
<intersection_of>
<to>SO:0000690</to>
</intersection_of>
<intersection_of>
<type>transcribed_to</type>
<to>SO:0000079</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000693</id>
<name>gene_with_recoded_mRNA</name>
<def>
<defstr>A gene that encodes an mRNA that is recoded.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with recoded mRNA</synonym_text>
</synonym>
<is_a>SO:0001217</is_a>
<intersection_of>
<to>SO:0001217</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000881</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000694</id>
<name>SNP</name>
<def>
<defstr>SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>single nucleotide polymorphism</synonym_text>
</synonym>
<is_a>SO:0001483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000695</id>
<name>reagent</name>
<def>
<defstr>A sequence used in experiment.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Requested by Lynn Crosby, jan 2006.</comment>
<subset>SOFA</subset>
<is_a>SO:0001409</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000696</id>
<name>oligo</name>
<def>
<defstr>A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>oligonucleotide</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Oligonucleotide</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000695</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000697</id>
<name>gene_with_stop_codon_read_through</name>
<def>
<defstr>A gene that encodes a transcript with stop codon readthrough.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with stop codon read through</synonym_text>
</synonym>
<is_a>SO:0000693</is_a>
<intersection_of>
<to>SO:0000693</to>
</intersection_of>
<intersection_of>
<type>has_part</type>
<to>SO:0000883</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000698</id>
<name>gene_with_stop_codon_redefined_as_pyrrolysine</name>
<def>
<defstr>A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with stop codon redefined as pyrrolysine</synonym_text>
</synonym>
<is_a>SO:0000697</is_a>
<intersection_of>
<to>SO:0000693</to>
</intersection_of>
<intersection_of>
<type>has_part</type>
<to>SO:0000884</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000699</id>
<name>junction</name>
<def>
<defstr>A sequence_feature with an extent of zero.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A junction is a boundary between regions. A boundary has an extent of zero.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>boundary</synonym_text>
</synonym>
<is_a>SO:0000110</is_a>
<disjoint_from>SO:0000001</disjoint_from>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000700</id>
<name>remark</name>
<def>
<defstr>A comment about the sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_a>SO:0001410</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000701</id>
<name>possible_base_call_error</name>
<def>
<defstr>A region of sequence where the validity of the base calling is questionable.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>possible base call error</synonym_text>
</synonym>
<is_a>SO:0000413</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000702</id>
<name>possible_assembly_error</name>
<def>
<defstr>A region of sequence where there may have been an error in the assembly.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>possible assembly error</synonym_text>
</synonym>
<is_a>SO:0000413</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000703</id>
<name>experimental_result_region</name>
<def>
<defstr>A region of sequence implicated in an experimental result.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>experimental result region</synonym_text>
</synonym>
<is_a>SO:0000700</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000704</id>
<name>gene</name>
<def>
<defstr>A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.</defstr>
<dbxref>
<acc>immuno_workshop</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.</comment>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Gene</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<relationship>
<type>member_of</type>
<to>SO:0005855</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000705</id>
<name>tandem_repeat</name>
<def>
<defstr>Two or more adjcent copies of a region (of length greater than 1).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>tandem repeat</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Tandem_repeat</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<xref_analog>
<acc>http://www.sci.sdsu.edu/~smaloy/Glossary/T.html</acc>
<dbname>URL</dbname>
</xref_analog>
<is_a>SO:0000657</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000706</id>
<name>trans_splice_acceptor_site</name>
<def>
<defstr>The 3' splice site of the acceptor primary transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.</comment>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>3' trans splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>trans splice acceptor site</synonym_text>
</synonym>
<is_a>SO:0001420</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000707</id>
<name>trans_splice_donor_site</name>
<def>
<defstr>The 5' five prime splice site region of the donor RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>SL RNA contains a donor site.</comment>
<synonym scope="related">
<synonym_text>5 prime trans splice site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>trans splice donor site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>trans-splice donor site</synonym_text>
</synonym>
<is_a>SO:0001420</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000708</id>
<name>SL1_acceptor_site</name>
<synonym scope="exact">
<synonym_text>SL1 acceptor site</synonym_text>
</synonym>
<is_a>SO:0000706</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000709</id>
<name>SL2_acceptor_site</name>
<synonym scope="exact">
<synonym_text>SL2 acceptor site</synonym_text>
</synonym>
<is_a>SO:0000706</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000710</id>
<name>gene_with_stop_codon_redefined_as_selenocysteine</name>
<def>
<defstr>A gene encoding an mRNA that has the stop codon redefined as selenocysteine.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with stop codon redefined as selenocysteine</synonym_text>
</synonym>
<is_a>SO:0000697</is_a>
<intersection_of>
<to>SO:0000697</to>
</intersection_of>
<intersection_of>
<type>has_part</type>
<to>SO:0000885</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000711</id>
<name>gene_with_mRNA_recoded_by_translational_bypass</name>
<def>
<defstr>A gene with mRNA recoded by translational bypass.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with mRNA recoded by translational bypass</synonym_text>
</synonym>
<is_a>SO:0000693</is_a>
<intersection_of>
<to>SO:0001217</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000886</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000712</id>
<name>gene_with_transcript_with_translational_frameshift</name>
<def>
<defstr>A gene encoding a transcript that has a translational frameshift.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene with transcript with translational frameshift</synonym_text>
</synonym>
<is_a>SO:0000693</is_a>
<intersection_of>
<to>SO:0000693</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000887</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000713</id>
<name>DNA_motif</name>
<def>
<defstr>A motif that is active in the DNA form of the sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>DNA motif</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/DNA_motif</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000714</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000714</id>
<name>nucleotide_motif</name>
<def>
<defstr>A region of nucleotide sequence corresponding to a known motif.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>nucleotide motif</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000715</id>
<name>RNA_motif</name>
<def>
<defstr>A motif that is active in RNA sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>RNA motif</synonym_text>
</synonym>
<is_a>SO:0000714</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000716</id>
<name>dicistronic_mRNA</name>
<def>
<defstr>An mRNA that has the quality dicistronic.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>dicistronic mRNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>dicistronic processed transcript</synonym_text>
</synonym>
<is_a>SO:0000079</is_a>
<is_a>SO:0000634</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000879</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000717</id>
<name>reading_frame</name>
<def>
<defstr>A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.</defstr>
<dbxref>
<acc>rb</acc>
<dbname>SGD</dbname>
</dbxref>
</def>
<comment>This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>reading frame</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Reading_frame</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001410</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000718</id>
<name>blocked_reading_frame</name>
<def>
<defstr>A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons.</defstr>
<dbxref>
<acc>rb</acc>
<dbname>SGD</dbname>
</dbxref>
</def>
<comment>Term requested by Rama from SGD.</comment>
<synonym scope="exact">
<synonym_text>blocked reading frame</synonym_text>
</synonym>
<is_a>SO:0000717</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000719</id>
<name>ultracontig</name>
<def>
<defstr>An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.</defstr>
<dbxref>
<acc>WG</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_a>SO:0000353</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000720</id>
<name>foreign_transposable_element</name>
<def>
<defstr>A transposable element that is foreign.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>requested by Michael on 19 Nov 2004.</comment>
<synonym scope="exact">
<synonym_text>foreign transposable element</synonym_text>
</synonym>
<is_a>SO:0000101</is_a>
<intersection_of>
<to>SO:0000101</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000784</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000721</id>
<name>gene_with_dicistronic_primary_transcript</name>
<def>
<defstr>A gene that encodes a dicistronic primary transcript.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Requested by Michael, 19 nov 2004.</comment>
<synonym scope="exact">
<synonym_text>gene with dicistronic primary transcript</synonym_text>
</synonym>
<is_a>SO:0000692</is_a>
<intersection_of>
<to>SO:0000692</to>
</intersection_of>
<intersection_of>
<type>transcribed_to</type>
<to>SO:1001197</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000722</id>
<name>gene_with_dicistronic_mRNA</name>
<def>
<defstr>A gene that encodes a polycistronic mRNA.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Requested by MA nov 19 2004.</comment>
<synonym scope="exact">
<synonym_text>gene with dicistronic mRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>gene with dicistronic processed transcript</synonym_text>
</synonym>
<is_a>SO:0000692</is_a>
<intersection_of>
<to>SO:0000692</to>
</intersection_of>
<intersection_of>
<type>transcribed_to</type>
<to>SO:0000716</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000723</id>
<name>iDNA</name>
<def>
<defstr>Genomic sequence removed from the genome, as a normal event, by a process of recombination.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>intervening DNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/IDNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000298</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000724</id>
<name>oriT</name>
<def>
<defstr>A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>origin of transfer</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Origin_of_transfer</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000296</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000725</id>
<name>transit_peptide</name>
<alt_id>BS:00055</alt_id>
<def>
<defstr>The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Added to bring SO inline with the embl ddbj genbank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.</comment>
<subset>biosapiens</subset>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>signal</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>transit</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>transit peptide</synonym_text>
</synonym>
<is_a>SO:0100011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000726</id>
<name>repeat_unit</name>
<def>
<defstr>The simplest repeated component of a repeat region. A single repeat.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Added to comply with the feature table. A single repeat.</comment>
<synonym scope="exact">
<synonym_text>repeat unit</synonym_text>
</synonym>
<xref_analog>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</xref_analog>
<is_a>SO:0001412</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000727</id>
<name>CRM</name>
<def>
<defstr>A regulatory_region where more than 1 TF_binding_site together are regulatorily active.</defstr>
<dbxref>
<acc>SG</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Requested by Stepen Grossmann Dec 2004.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>cis regulatory module</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>TF module</synonym_text>
</synonym>
<is_a>SO:0001055</is_a>
<intersection_of>
<to>SO:0001055</to>
</intersection_of>
<intersection_of>
<type>has_part</type>
<to>SO:0000235</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000728</id>
<name>intein</name>
<def>
<defstr>A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Intein-mediated protein splicing occurs after mRNA has been translated into a protein.</comment>
<synonym scope="related">
<synonym_text>protein intron</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Intein</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0100011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000729</id>
<name>intein_containing</name>
<def>
<defstr>An attribute of protein-coding genes where the initial protein product contains an intein.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>intein containing</synonym_text>
</synonym>
<is_a>SO:0000010</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000730</id>
<name>gap</name>
<def>
<defstr>A gap in the sequence of known length. The unknown bases are filled in with N's.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_a>SO:0000143</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000353</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000731</id>
<name>fragmentary</name>
<def>
<defstr>An attribute to describe a feature that is incomplete.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Term added because of request by MO people.</comment>
<synonym scope="exact">
<synonym_text>fragment</synonym_text>
</synonym>
<is_a>SO:0000905</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000732</id>
<name>predicted</name>
<def>
<defstr>An attribute describing an unverified region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Predicted</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000905</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000733</id>
<name>feature_attribute</name>
<def>
<defstr>An attribute describing a located_sequence_feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>feature attribute</synonym_text>
</synonym>
<is_a>SO:0000400</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000734</id>
<name>exemplar_mRNA</name>
<def>
<defstr>An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.</defstr>
<dbxref>
<acc>http://mged.sourceforge.net/ontologies/MGEDontology.php</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Added for the MO people.</comment>
<synonym scope="exact">
<synonym_text>exemplar mRNA</synonym_text>
</synonym>
<is_a>SO:0000234</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000864</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000735</id>
<name>sequence_location</name>
<synonym scope="exact">
<synonym_text>sequence location</synonym_text>
</synonym>
<is_a>SO:0000400</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000736</id>
<name>organelle_sequence</name>
<synonym scope="exact">
<synonym_text>organelle sequence</synonym_text>
</synonym>
<is_a>SO:0000735</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000737</id>
<name>mitochondrial_sequence</name>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>mitochondrial sequence</synonym_text>
</synonym>
<is_a>SO:0000736</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000738</id>
<name>nuclear_sequence</name>
<synonym scope="exact">
<synonym_text>nuclear sequence</synonym_text>
</synonym>
<is_a>SO:0000736</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000739</id>
<name>nucleomorphic_sequence</name>
<synonym scope="exact">
<synonym_text>nucleomorphic sequence</synonym_text>
</synonym>
<is_a>SO:0000736</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000740</id>
<name>plastid_sequence</name>
<synonym scope="exact">
<synonym_text>plastid sequence</synonym_text>
</synonym>
<is_a>SO:0000736</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000741</id>
<name>kinetoplast</name>
<alt_id>SO:0000826</alt_id>
<def>
<defstr>A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species.</defstr>
<dbxref>
<acc>8395055</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>kinetoplast_chromosome</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Kinetoplast</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001260</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000742</id>
<name>maxicircle</name>
<alt_id>SO:0000827</alt_id>
<def>
<defstr>A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.</defstr>
<dbxref>
<acc>8395055</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>maxicircle_chromosome</synonym_text>
</synonym>
<is_a>SO:0001235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000741</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000743</id>
<name>apicoplast_sequence</name>
<synonym scope="exact">
<synonym_text>apicoplast sequence</synonym_text>
</synonym>
<is_a>SO:0000740</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000744</id>
<name>chromoplast_sequence</name>
<synonym scope="exact">
<synonym_text>chromoplast sequence</synonym_text>
</synonym>
<is_a>SO:0000740</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000745</id>
<name>chloroplast_sequence</name>
<synonym scope="exact">
<synonym_text>chloroplast sequence</synonym_text>
</synonym>
<is_a>SO:0000740</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000746</id>
<name>cyanelle_sequence</name>
<synonym scope="exact">
<synonym_text>cyanelle sequence</synonym_text>
</synonym>
<is_a>SO:0000740</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000747</id>
<name>leucoplast_sequence</name>
<synonym scope="exact">
<synonym_text>leucoplast sequence</synonym_text>
</synonym>
<is_a>SO:0000740</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000748</id>
<name>proplastid_sequence</name>
<synonym scope="exact">
<synonym_text>proplastid sequence</synonym_text>
</synonym>
<is_a>SO:0000740</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000749</id>
<name>plasmid_location</name>
<synonym scope="exact">
<synonym_text>plasmid location</synonym_text>
</synonym>
<is_a>SO:0000735</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000750</id>
<name>amplification_origin</name>
<def>
<defstr>An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>amplification origin</synonym_text>
</synonym>
<is_a>SO:0000296</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000751</id>
<name>proviral_location</name>
<synonym scope="exact">
<synonym_text>proviral location</synonym_text>
</synonym>
<is_a>SO:0000735</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000752</id>
<name>gene_group_regulatory_region</name>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>gene group regulatory region</synonym_text>
</synonym>
<is_a>SO:0005836</is_a>
<relationship>
<type>member_of</type>
<to>SO:0005855</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000753</id>
<name>clone_insert</name>
<def>
<defstr>The region of sequence that has been inserted and is being propogated by the clone.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>clone insert</synonym_text>
</synonym>
<is_a>SO:0000695</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000151</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000754</id>
<name>lambda_vector</name>
<def>
<defstr>The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.</defstr>
<dbxref>
<acc>0-1767-2380-8</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>lambda vector</synonym_text>
</synonym>
<is_a>SO:0000440</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000755</id>
<name>plasmid_vector</name>
<synonym scope="exact">
<synonym_text>plasmid vector</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Plasmid_vector#Vectors</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000440</is_a>
<intersection_of>
<to>SO:0001235</to>
</intersection_of>
<intersection_of>
<type>derives_from</type>
<to>SO:0000155</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000756</id>
<name>cDNA</name>
<def>
<defstr>DNA synthesized by reverse transcriptase using RNA as a template.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/CDNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000352</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000757</id>
<name>single_stranded_cDNA</name>
<synonym scope="exact">
<synonym_text>single strand cDNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>single stranded cDNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>single-strand cDNA</synonym_text>
</synonym>
<is_a>SO:0000756</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000758</id>
<name>double_stranded_cDNA</name>
<synonym scope="related">
<synonym_text>double strand cDNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>double stranded cDNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>double-strand cDNA</synonym_text>
</synonym>
<is_a>SO:0000756</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000759</id>
<name>plasmid_clone</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000760</id>
<name>YAC_clone</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000761</id>
<name>phagemid_clone</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000762</id>
<name>PAC_clone</name>
<synonym scope="related">
<synonym_text>P1_clone</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000763</id>
<name>fosmid_clone</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000764</id>
<name>BAC_clone</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000765</id>
<name>cosmid_clone</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000766</id>
<name>pyrrolysyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>pyrrolysyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>pyrrolysyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>pyrrolysyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0001178</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000767</id>
<name>clone_insert_start</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000768</id>
<name>episome</name>
<def>
<defstr>A plasmid that may integrate with a chromosome.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000155</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000769</id>
<name>tmRNA_coding_piece</name>
<def>
<defstr>The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.</defstr>
<dbxref>
<acc>10.1093/nar/gkh795</acc>
<dbname>doi</dbname>
</dbxref>
<dbxref>
<acc>kw</acc>
<dbname>Indiana</dbname>
</dbxref>
<dbxref>
<acc>1362-4962</acc>
<dbname>issn</dbname>
</dbxref>
</def>
<comment>Added in response to comment from Kelly Williams from Indiana. Nov 2005.</comment>
<synonym scope="exact">
<synonym_text>tmRNA coding piece</synonym_text>
</synonym>
<is_a>SO:0000847</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000770</id>
<name>tmRNA_acceptor_piece</name>
<def>
<defstr>The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.</defstr>
<dbxref>
<acc>10.1093/nar/gkh795</acc>
<dbname>doi</dbname>
</dbxref>
<dbxref>
<acc>kw</acc>
<dbname>Indiana</dbname>
</dbxref>
</def>
<comment>Added in response to Kelly Williams from Indiana. Date: Nov 2005.</comment>
<synonym scope="exact">
<synonym_text>tmRNA acceptor piece</synonym_text>
</synonym>
<is_a>SO:0000847</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000771</id>
<name>QTL</name>
<def>
<defstr>A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.</defstr>
<dbxref>
<acc>http://rgd.mcw.edu/tu/qtls/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Added in respose to request by Simon Twigger November 14th 2005.</comment>
<synonym scope="exact">
<synonym_text>quantitative trait locus</synonym_text>
</synonym>
<is_a>SO:0001410</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000772</id>
<name>genomic_island</name>
<def>
<defstr>A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.</defstr>
<dbxref>
<acc>at</acc>
<dbname>Phigo</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Genomic islands are transmissible elements characterized by large size (>10kb).</comment>
<synonym scope="exact">
<synonym_text>genomic island</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Genomic_island</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001039</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000773</id>
<name>pathogenic_island</name>
<def>
<defstr>Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.</comment>
<synonym scope="exact">
<synonym_text>pathogenic island</synonym_text>
</synonym>
<is_a>SO:0000772</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000774</id>
<name>metabolic_island</name>
<def>
<defstr>A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.</comment>
<synonym scope="exact">
<synonym_text>metabolic island</synonym_text>
</synonym>
<is_a>SO:0000772</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000775</id>
<name>adaptive_island</name>
<def>
<defstr>An adaptive island is a genomic island that provides an adaptive advantage to the host.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.</comment>
<synonym scope="exact">
<synonym_text>adaptive island</synonym_text>
</synonym>
<is_a>SO:0000772</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000776</id>
<name>symbiosis_island</name>
<def>
<defstr>A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149.</comment>
<synonym scope="exact">
<synonym_text>symbiosis island</synonym_text>
</synonym>
<is_a>SO:0000772</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000777</id>
<name>pseudogenic_rRNA</name>
<def>
<defstr>A non functional descendent of an rRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>pseudogenic rRNA</synonym_text>
</synonym>
<is_a>SO:0000462</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000778</id>
<name>pseudogenic_tRNA</name>
<def>
<defstr>A non functional descendent of a tRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>pseudogenic tRNA</synonym_text>
</synonym>
<is_a>SO:0000462</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000779</id>
<name>engineered_episome</name>
<def>
<defstr>An episome that is engineered.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Requested by Lynn Crosby Jan 2006.</comment>
<synonym scope="exact">
<synonym_text>engineered episome</synonym_text>
</synonym>
<is_a>SO:0000637</is_a>
<is_a>SO:0000768</is_a>
<intersection_of>
<to>SO:0000768</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000780</id>
<name>transposable_element_attribute</name>
<comment>Added by KE Jan 2006 to capture the kinds of attributes of TEs</comment>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000781</id>
<name>transgenic</name>
<def>
<defstr>Attribute describing sequence that has been integrated with foreign sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000782</id>
<name>natural</name>
<def>
<defstr>An attribute describing a feature that occurs in nature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000783</id>
<name>engineered</name>
<def>
<defstr>An attribute to describe a region that was modified in vitro.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000784</id>
<name>foreign</name>
<def>
<defstr>An attribute to describe a region from another species.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000785</id>
<name>cloned_region</name>
<comment>Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.</comment>
<synonym scope="exact">
<synonym_text>cloned region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>cloned segment</synonym_text>
</synonym>
<is_a>SO:0000695</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000753</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000786</id>
<name>reagent_attribute</name>
<comment>Added jan 2006 by KE.</comment>
<synonym scope="exact">
<synonym_text>reagent attribute</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000787</id>
<name>clone_attribute</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000788</id>
<name>cloned</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000789</id>
<name>validated</name>
<def>
<defstr>An attribute to describe a feature that has been proven.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000905</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000790</id>
<name>invalidated</name>
<def>
<defstr>An attribute describing a feature that is invalidated.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000905</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000791</id>
<name>cloned_genomic</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000792</id>
<name>cloned_cDNA</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000793</id>
<name>engineered_DNA</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000794</id>
<name>engineered_rescue_region</name>
<def>
<defstr>A rescue region that is engineered.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered rescue fragment</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>engineered rescue region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>engineered rescue segment</synonym_text>
</synonym>
<is_a>SO:0000411</is_a>
<is_a>SO:0000804</is_a>
<intersection_of>
<to>SO:0000411</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000795</id>
<name>rescue_mini_gene</name>
<def>
<defstr>A mini_gene that rescues.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>rescue mini gene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rescue mini-gene</synonym_text>
</synonym>
<is_a>SO:0000815</is_a>
<intersection_of>
<to>SO:0000815</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000814</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000796</id>
<name>transgenic_transposable_element</name>
<def>
<defstr>TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.</defstr>
<dbxref>
<acc>mc</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<comment>Modified as requested by Lynn - FB. May 2007.</comment>
<synonym scope="exact">
<synonym_text>transgenic transposable element</synonym_text>
</synonym>
<is_a>SO:0000101</is_a>
<intersection_of>
<to>SO:0000101</to>
</intersection_of>
<intersection_of>
<type>derives_from</type>
<to>SO:0000151</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000781</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000797</id>
<name>natural_transposable_element</name>
<def>
<defstr>TE that exists (or existed) in nature.</defstr>
<dbxref>
<acc>mc</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>natural transposable element</synonym_text>
</synonym>
<is_a>SO:0000101</is_a>
<is_a>SO:0001476</is_a>
<intersection_of>
<to>SO:0000101</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000782</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000798</id>
<name>engineered_transposable_element</name>
<def>
<defstr>TE that has been modified by manipulations in vitro.</defstr>
<dbxref>
<acc>mc</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered transposable element</synonym_text>
</synonym>
<is_a>SO:0000101</is_a>
<is_a>SO:0000804</is_a>
<intersection_of>
<to>SO:0000101</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000799</id>
<name>engineered_foreign_transposable_element</name>
<def>
<defstr>A transposable_element that is engineered and foreign.</defstr>
<dbxref>
<acc>mc</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered foreign transposable element</synonym_text>
</synonym>
<is_a>SO:0000720</is_a>
<is_a>SO:0000798</is_a>
<is_a>SO:0000805</is_a>
<intersection_of>
<to>SO:0000101</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000784</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000800</id>
<name>assortment_derived_duplication</name>
<def>
<defstr>A multi-chromosome duplication aberration generated by reassortment of other aberration components.</defstr>
<dbxref>
<acc>gm</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>assortment derived duplication</synonym_text>
</synonym>
<is_a>SO:0000240</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000801</id>
<name>assortment_derived_deficiency_plus_duplication</name>
<def>
<defstr>A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.</defstr>
<dbxref>
<acc>gm</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>assortment derived deficiency plus duplication</synonym_text>
</synonym>
<is_a>SO:0000240</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000802</id>
<name>assortment_derived_deficiency</name>
<def>
<defstr>A multi-chromosome deficiency aberration generated by reassortment of other aberration components.</defstr>
<dbxref>
<acc>gm</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>assortment-derived deficiency</synonym_text>
</synonym>
<is_a>SO:0000240</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000803</id>
<name>assortment_derived_aneuploid</name>
<def>
<defstr>A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.</defstr>
<dbxref>
<acc>gm</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>assortment derived aneuploid</synonym_text>
</synonym>
<is_a>SO:0000240</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000804</id>
<name>engineered_region</name>
<def>
<defstr>A region that is engineered.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>engineered sequence</synonym_text>
</synonym>
<is_a>SO:0001409</is_a>
<intersection_of>
<to>SO:0000001</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000805</id>
<name>engineered_foreign_region</name>
<def>
<defstr>A region that is engineered and foreign.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered foreign region</synonym_text>
</synonym>
<is_a>SO:0000804</is_a>
<intersection_of>
<to>SO:0000001</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000784</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000806</id>
<name>fusion</name>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000807</id>
<name>engineered_tag</name>
<def>
<defstr>A tag that is engineered.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered tag</synonym_text>
</synonym>
<is_a>SO:0000324</is_a>
<is_a>SO:0000804</is_a>
<intersection_of>
<to>SO:0000324</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000808</id>
<name>validated_cDNA_clone</name>
<def>
<defstr>A cDNA clone that has been validated.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>validated cDNA clone</synonym_text>
</synonym>
<is_a>SO:0000317</is_a>
<intersection_of>
<to>SO:0000317</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000789</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000809</id>
<name>invalidated_cDNA_clone</name>
<def>
<defstr>A cDNA clone that is invalid.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>invalidated cDNA clone</synonym_text>
</synonym>
<is_a>SO:0000317</is_a>
<intersection_of>
<to>SO:0000317</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000790</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000810</id>
<name>chimeric_cDNA_clone</name>
<def>
<defstr>A cDNA clone invalidated because it is chimeric.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>chimeric cDNA clone</synonym_text>
</synonym>
<is_a>SO:0000809</is_a>
<intersection_of>
<to>SO:0000809</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000362</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000811</id>
<name>genomically_contaminated_cDNA_clone</name>
<def>
<defstr>A cDNA clone invalidated by genomic contamination.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>genomically contaminated cDNA clone</synonym_text>
</synonym>
<is_a>SO:0000809</is_a>
<intersection_of>
<to>SO:0000809</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000414</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000812</id>
<name>polyA_primed_cDNA_clone</name>
<def>
<defstr>A cDNA clone invalidated by polyA priming.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>polyA primed cDNA clone</synonym_text>
</synonym>
<is_a>SO:0000809</is_a>
<intersection_of>
<to>SO:0000809</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000415</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000813</id>
<name>partially_processed_cDNA_clone</name>
<def>
<defstr>A cDNA invalidated clone by partial processing.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>partially processed cDNA clone</synonym_text>
</synonym>
<is_a>SO:0000809</is_a>
<intersection_of>
<to>SO:0000809</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000416</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000814</id>
<name>rescue</name>
<def>
<defstr>An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000815</id>
<name>mini_gene</name>
<def>
<defstr>By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA.</defstr>
<dbxref>
<acc>15992143</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mini gene</synonym_text>
</synonym>
<is_a>SO:0000236</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000816</id>
<name>rescue_gene</name>
<def>
<defstr>A gene that rescues.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>rescue gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000814</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000817</id>
<name>wild_type</name>
<def>
<defstr>An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>wild type</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Wild_type</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000818</id>
<name>wild_type_rescue_gene</name>
<def>
<defstr>A gene that rescues.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>wild type rescue gene</synonym_text>
</synonym>
<is_a>SO:0000816</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000817</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000819</id>
<name>mitochondrial_chromosome</name>
<def>
<defstr>A chromosome originating in a mitochondria.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mitochondrial chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000737</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000820</id>
<name>chloroplast_chromosome</name>
<def>
<defstr>A chromosome originating in a chloroplast.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>chloroplast chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000745</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000821</id>
<name>chromoplast_chromosome</name>
<def>
<defstr>A chromosome originating in a chromoplast.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>chromoplast chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000744</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000822</id>
<name>cyanelle_chromosome</name>
<def>
<defstr>A chromosome originating in a cyanelle.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cyanelle chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000746</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000823</id>
<name>leucoplast_chromosome</name>
<def>
<defstr>A chromosome with origin in a leucoplast.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>leucoplast chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000747</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000824</id>
<name>macronuclear_chromosome</name>
<def>
<defstr>A chromosome originating in a macronucleus.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>macronuclear chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000083</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000825</id>
<name>micronuclear_chromosome</name>
<def>
<defstr>A chromosome originating in a micronucleus.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>micronuclear chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000084</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000828</id>
<name>nuclear_chromosome</name>
<def>
<defstr>A chromosome originating in a nucleus.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>nuclear chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000738</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000829</id>
<name>nucleomorphic_chromosome</name>
<def>
<defstr>A chromosome originating in a nucleomorph.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>nucleomorphic chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000739</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000830</id>
<name>chromosome_part</name>
<def>
<defstr>A region of a chromosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>chromosome part</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000340</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000831</id>
<name>gene_member_region</name>
<def>
<defstr>A region of a gene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A manufactured term used to allow the parts of a gene to have an is_a path to the root.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>gene member region</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<relationship>
<type>member_of</type>
<to>SO:0000704</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000832</id>
<name>promoter_region</name>
<def>
<defstr>A region of sequence which is part of a promoter.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.</comment>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000833</id>
<name>transcript_region</name>
<def>
<defstr>A region of a transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>transcript region</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000673</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000834</id>
<name>mature_transcript_region</name>
<def>
<defstr>A region of a mature transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>mature transcript region</synonym_text>
</synonym>
<is_a>SO:0000833</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000835</id>
<name>primary_transcript_region</name>
<def>
<defstr>A part of a primary transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>primary transcript region</synonym_text>
</synonym>
<is_a>SO:0000833</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000185</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000836</id>
<name>mRNA_region</name>
<def>
<defstr>A region of an mRNA.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>mRNA region</synonym_text>
</synonym>
<is_a>SO:0000834</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000234</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000837</id>
<name>UTR_region</name>
<def>
<defstr>A region of UTR.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>UTR region</synonym_text>
</synonym>
<is_a>SO:0000836</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000838</id>
<name>rRNA_primary_transcript_region</name>
<def>
<defstr>A region of an rRNA primary transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>To allow transcribed_spacer_region to have a path to the root.</comment>
<synonym scope="exact">
<synonym_text>rRNA primary transcript region</synonym_text>
</synonym>
<is_a>SO:0000835</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000209</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000839</id>
<name>polypeptide_region</name>
<alt_id>BS:00124</alt_id>
<alt_id>BS:00331</alt_id>
<def>
<defstr>Biological sequence region that can be assigned to a specific subsequence of a polypeptide.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>SO</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Added to allow the polypeptide regions to have is_a paths back to the root.</comment>
<subset>biosapiens</subset>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>positional</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>positional polypeptide feature</synonym_text>
</synonym>
<synonym scope="narrow">
<synonym_text>region</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="related">
<synonym_text>region or site annotation</synonym_text>
</synonym>
<synonym scope="narrow">
<synonym_text>site</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<is_a>SO:0001411</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000104</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000840</id>
<name>repeat_component</name>
<def>
<defstr>A region of a repeated sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A manufactured to group the parts of repeats, to give them an is_a path back to the root.</comment>
<synonym scope="exact">
<synonym_text>repeat component</synonym_text>
</synonym>
<is_a>SO:0001412</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000841</id>
<name>spliceosomal_intron_region</name>
<def>
<defstr>A region within an intron.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A terms added to allow the parts of introns to have is_a paths to the root.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>spliceosomal intron region</synonym_text>
</synonym>
<is_a>SO:0000835</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000662</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000842</id>
<name>gene_component_region</name>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>gene component region</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000704</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000843</id>
<name>bacterial_RNApol_promoter_region</name>
<def>
<defstr>A region which is part of a bacterial RNA polymerase promoter.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.</comment>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000844</id>
<name>RNApol_II_promoter_region</name>
<def>
<defstr>A region of sequence which is a promoter for RNA polymerase II.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.</comment>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000845</id>
<name>RNApol_III_promoter_type_1_region</name>
<def>
<defstr>A region of sequence which is a promoter for RNA polymerase III type 1.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.</comment>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000846</id>
<name>RNApol_III_promoter_type_2_region</name>
<def>
<defstr>A region of sequence which is a promoter for RNA polymerase III type 2.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.</comment>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000847</id>
<name>tmRNA_region</name>
<def>
<defstr>A region of a tmRNA.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.</comment>
<synonym scope="exact">
<synonym_text>tmRNA region</synonym_text>
</synonym>
<is_a>SO:0000834</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000584</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000848</id>
<name>LTR_component</name>
<synonym scope="exact">
<synonym_text>long term repeat component</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>LTR component</synonym_text>
</synonym>
<is_a>SO:0000840</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000286</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000849</id>
<name>three_prime_LTR_component</name>
<synonym scope="exact">
<synonym_text>3' long terminal repeat component</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime LTR component</synonym_text>
</synonym>
<is_a>SO:0000848</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000426</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000850</id>
<name>five_prime_LTR_component</name>
<synonym scope="exact">
<synonym_text>5' long term repeat component</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime LTR component</synonym_text>
</synonym>
<is_a>SO:0000848</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000425</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000851</id>
<name>CDS_region</name>
<def>
<defstr>A region of a CDS.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>CDS region</synonym_text>
</synonym>
<is_a>SO:0000836</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000316</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000852</id>
<name>exon_region</name>
<def>
<defstr>A region of an exon.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>exon region</synonym_text>
</synonym>
<is_a>SO:0000833</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000147</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000853</id>
<name>homologous_region</name>
<def>
<defstr>A region that is homologous to another region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>homolog</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>homologous region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>homologue</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Homology_(biology)</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000330</is_a>
<intersection_of>
<to>SO:0000330</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000857</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000854</id>
<name>paralogous_region</name>
<def>
<defstr>A homologous_region that is paralogous to another region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A term to be used in conjunction with the paralogous_to relationship.</comment>
<synonym scope="exact">
<synonym_text>paralog</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>paralogous region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>paralogue</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Paralog#Paralogy</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000853</is_a>
<intersection_of>
<to>SO:0000853</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000859</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000855</id>
<name>orthologous_region</name>
<def>
<defstr>A homologous_region that is orthologous to another region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term should be used in conjunction with the similarity relationships defined in SO.</comment>
<synonym scope="exact">
<synonym_text>ortholog</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>orthologous region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>orthologue</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Ortholog#Orthology</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000853</is_a>
<intersection_of>
<to>SO:0000853</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000858</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000856</id>
<name>conserved</name>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000857</id>
<name>homologous</name>
<def>
<defstr>Similarity due to common ancestry.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000856</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000858</id>
<name>orthologous</name>
<def>
<defstr>An attribute describing a kind of homology where divergence occured after a speciation event.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000857</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000859</id>
<name>paralogous</name>
<def>
<defstr>An attribute describing a kind of homology where divergence occurred after a duplication event.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000857</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000860</id>
<name>syntenic</name>
<def>
<defstr>Attribute describing sequence regions occurring in same order on chromosome of different species.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Syntenic</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000856</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000861</id>
<name>capped_primary_transcript</name>
<def>
<defstr>A primary transcript that is capped.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>capped primary transcript</synonym_text>
</synonym>
<is_a>SO:0000185</is_a>
<intersection_of>
<to>SO:0000185</to>
</intersection_of>
<intersection_of>
<type>adjacent_to</type>
<to>SO:0000581</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000146</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000862</id>
<name>capped_mRNA</name>
<def>
<defstr>An mRNA that is capped.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>capped mRNA</synonym_text>
</synonym>
<is_a>SO:0000234</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>adjacent_to</type>
<to>SO:0000581</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000146</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000863</id>
<name>mRNA_attribute</name>
<def>
<defstr>An attribute describing an mRNA feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mRNA attribute</synonym_text>
</synonym>
<is_a>SO:0000237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000864</id>
<name>exemplar</name>
<def>
<defstr>An attribute describing a sequence is representative of a class of similar sequences.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000863</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000865</id>
<name>frameshift</name>
<def>
<defstr>An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Frameshift</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000863</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000866</id>
<name>minus_1_frameshift</name>
<def>
<defstr>A frameshift caused by deleting one base.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>minus 1 frameshift</synonym_text>
</synonym>
<is_a>SO:0000865</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000867</id>
<name>minus_2_frameshift</name>
<def>
<defstr>A frameshift caused by deleting two bases.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>minus 2 frameshift</synonym_text>
</synonym>
<is_a>SO:0000865</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000868</id>
<name>plus_1_frameshift</name>
<def>
<defstr>A frameshift caused by inserting one base.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>plus 1 frameshift</synonym_text>
</synonym>
<is_a>SO:0000865</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000869</id>
<name>plus_2_framshift</name>
<def>
<defstr>A frameshift caused by inserting two bases.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>plus 2 framshift</synonym_text>
</synonym>
<is_a>SO:0000865</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000870</id>
<name>trans_spliced</name>
<def>
<defstr>An attribute describing transcript sequence that is created by splicing exons from diferent genes.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>trans-spliced</synonym_text>
</synonym>
<is_a>SO:0000237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000871</id>
<name>polyadenylated_mRNA</name>
<def>
<defstr>An mRNA that is polyadenylated.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>polyadenylated mRNA</synonym_text>
</synonym>
<is_a>SO:0000234</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>adjacent_to</type>
<to>SO:0000610</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000246</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000872</id>
<name>trans_spliced_mRNA</name>
<def>
<defstr>An mRNA that is trans-spliced.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>trans-spliced mRNA</synonym_text>
</synonym>
<is_a>SO:0000234</is_a>
<is_a>SO:0000479</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>adjacent_to</type>
<to>SO:0000636</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000870</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000873</id>
<name>edited_transcript</name>
<def>
<defstr>A transcript that is edited.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>edited transcript</synonym_text>
</synonym>
<is_a>SO:0000673</is_a>
<intersection_of>
<to>SO:0000673</to>
</intersection_of>
<intersection_of>
<type>guided_by</type>
<to>SO:0000602</to>
</intersection_of>
<intersection_of>
<type>has_part</type>
<to>SO:0000977</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000116</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000874</id>
<name>edited_transcript_by_A_to_I_substitution</name>
<def>
<defstr>A transcript that has been edited by A to I substitution.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>edited transcript by A to I substitution</synonym_text>
</synonym>
<is_a>SO:0000873</is_a>
<is_a>SO:0000929</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000875</id>
<name>bound_by_protein</name>
<def>
<defstr>An attribute describing a sequence that is bound by a protein.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>bound by protein</synonym_text>
</synonym>
<is_a>SO:0000277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000876</id>
<name>bound_by_nucleic_acid</name>
<def>
<defstr>An attribute describing a sequence that is bound by a nucleic acid.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>bound by nucleic acid</synonym_text>
</synonym>
<is_a>SO:0000277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000877</id>
<name>alternatively_spliced</name>
<def>
<defstr>An attribute describing a situation where a gene may encode for more than 1 transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>alternatively spliced</synonym_text>
</synonym>
<is_a>SO:0000237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000878</id>
<name>monocistronic</name>
<def>
<defstr>An attribute describing a sequence that contains the code for one gene product.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000879</id>
<name>dicistronic</name>
<def>
<defstr>An attribute describing a sequence that contains the code for two gene products.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000880</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000880</id>
<name>polycistronic</name>
<def>
<defstr>An attribute describing a sequence that contains the code for more than one gene product.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000881</id>
<name>recoded</name>
<def>
<defstr>An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000863</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000882</id>
<name>codon_redefined</name>
<def>
<defstr>An attribute describing the alteration of codon meaning.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>codon redefined</synonym_text>
</synonym>
<is_a>SO:0000881</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000883</id>
<name>stop_codon_read_through</name>
<def>
<defstr>A stop codon redefined to be a new amino acid.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>stop codon read through</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>stop codon readthrough</synonym_text>
</synonym>
<is_a>SO:0000145</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000884</id>
<name>stop_codon_redefined_as_pyrrolysine</name>
<def>
<defstr>A stop codon redefined to be the new amino acid, pyrrolysine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>stop codon redefined as pyrrolysine</synonym_text>
</synonym>
<is_a>SO:0000883</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000885</id>
<name>stop_codon_redefined_as_selenocysteine</name>
<def>
<defstr>A stop codon redefined to be the new amino acid, selenocysteine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>stop codon redefined as selenocysteine</synonym_text>
</synonym>
<is_a>SO:0000883</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000886</id>
<name>recoded_by_translational_bypass</name>
<def>
<defstr>Recoded mRNA where a block of nucleotides is not translated.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>recoded by translational bypass</synonym_text>
</synonym>
<is_a>SO:0000881</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000887</id>
<name>translationally_frameshifted</name>
<def>
<defstr>Recoding by frameshifting a particular site.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>translationally frameshifted</synonym_text>
</synonym>
<is_a>SO:0000881</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000888</id>
<name>maternally_imprinted_gene</name>
<def>
<defstr>A gene that is maternally_imprinted.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>maternally imprinted gene</synonym_text>
</synonym>
<is_a>SO:0000898</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000135</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000889</id>
<name>paternally_imprinted_gene</name>
<def>
<defstr>A gene that is paternally imprinted.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>paternally imprinted gene</synonym_text>
</synonym>
<is_a>SO:0000898</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000136</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000890</id>
<name>post_translationally_regulated_gene</name>
<def>
<defstr>A gene that is post translationally regulated.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>post translationally regulated gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000130</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000891</id>
<name>negatively_autoregulated_gene</name>
<def>
<defstr>A gene that is negatively autoreguated.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>negatively autoregulated gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000473</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000892</id>
<name>positively_autoregulated_gene</name>
<def>
<defstr>A gene that is positively autoregulated.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>positively autoregulated gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000475</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000893</id>
<name>silenced</name>
<def>
<defstr>An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Silenced</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000126</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000894</id>
<name>silenced_by_DNA_modification</name>
<def>
<defstr>An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>silenced by DNA modification</synonym_text>
</synonym>
<is_a>SO:0000893</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000895</id>
<name>silenced_by_DNA_methylation</name>
<def>
<defstr>An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>silenced by DNA methylation</synonym_text>
</synonym>
<is_a>SO:0000894</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000896</id>
<name>translationally_regulated_gene</name>
<def>
<defstr>A gene that is translationally regulated.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>translationally regulated gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000131</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000897</id>
<name>allelically_excluded_gene</name>
<def>
<defstr>A gene that is allelically_excluded.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>allelically excluded gene</synonym_text>
</synonym>
<is_a>SO:0000898</is_a>
<intersection_of>
<to>SO:0000898</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000137</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000898</id>
<name>epigenetically_modified_gene</name>
<def>
<defstr>A gene that is epigenetically modified.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>epigenetically modified gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000133</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000899</id>
<name>nuclear_mitochondrial</name>
<def>
<defstr>An attribute describing a nuclear pseudogene of a mitochndrial gene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>nuclear mitochondrial</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000900</id>
<name>processed</name>
<def>
<defstr>An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000901</id>
<name>unequally_crossed_over</name>
<def>
<defstr>An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>unequally crossed over</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000902</id>
<name>transgene</name>
<def>
<defstr>A gene that is transgenic.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Transgene</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000781</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000903</id>
<name>endogenous_retroviral_sequence</name>
<synonym scope="exact">
<synonym_text>endogenous retroviral sequence</synonym_text>
</synonym>
<is_a>SO:0000751</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000904</id>
<name>rearranged_at_DNA_level</name>
<def>
<defstr>An attribute to describe the sequence of a feature, where the DNA is rearranged.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>rearranged at DNA level</synonym_text>
</synonym>
<is_a>SO:0000133</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000905</id>
<name>status</name>
<def>
<defstr>An attribute describing the status of a feature, based on the available evidence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term is the hypernym of attributes and should not be annotated to.</comment>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000906</id>
<name>independently_known</name>
<def>
<defstr>Attribute to describe a feature that is independently known - not predicted.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>independently known</synonym_text>
</synonym>
<is_a>SO:0000905</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000907</id>
<name>supported_by_sequence_similarity</name>
<def>
<defstr>An attribute to describe a feature that has been predicted using sequence similarity techniques.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>supported by sequence similarity</synonym_text>
</synonym>
<is_a>SO:0000732</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000908</id>
<name>supported_by_domain_match</name>
<def>
<defstr>An attribute to describe a feature that has been predicted using sequence similarity of a known domain.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>supported by domain match</synonym_text>
</synonym>
<is_a>SO:0000907</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000909</id>
<name>supported_by_EST_or_cDNA</name>
<def>
<defstr>An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>supported by EST or cDNA</synonym_text>
</synonym>
<is_a>SO:0000907</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000910</id>
<name>orphan</name>
<is_a>SO:0000732</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000911</id>
<name>predicted_by_ab_initio_computation</name>
<def>
<defstr>An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>predicted by ab initio computation</synonym_text>
</synonym>
<is_a>SO:0000732</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000912</id>
<name>asx_turn</name>
<alt_id>BS:00203</alt_id>
<def>
<defstr>A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>asx turn</synonym_text>
</synonym>
<is_a>SO:0001128</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000913</id>
<name>cloned_cDNA_insert</name>
<def>
<defstr>A clone insert made from cDNA.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cloned cDNA insert</synonym_text>
</synonym>
<is_a>SO:0000753</is_a>
<intersection_of>
<to>SO:0000753</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000756</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000914</id>
<name>cloned_genomic_insert</name>
<def>
<defstr>A clone insert made from genomic DNA.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cloned genomic insert</synonym_text>
</synonym>
<is_a>SO:0000753</is_a>
<intersection_of>
<to>SO:0000753</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000991</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000915</id>
<name>engineered_insert</name>
<def>
<defstr>A clone insert that is engineered.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>engineered insert</synonym_text>
</synonym>
<is_a>SO:0000753</is_a>
<is_a>SO:0000804</is_a>
<intersection_of>
<to>SO:0000753</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000783</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000916</id>
<name>edit_operation</name>
<synonym scope="exact">
<synonym_text>edit operation</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000917</id>
<name>insert_U</name>
<def>
<defstr>An edit to insert a U.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.</comment>
<synonym scope="exact">
<synonym_text>insert U</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000918</id>
<name>delete_U</name>
<def>
<defstr>An edit to delete a uridine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.</comment>
<synonym scope="exact">
<synonym_text>delete U</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000919</id>
<name>substitute_A_to_I</name>
<def>
<defstr>An edit to substitute an I for an A.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>substitute A to I</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000920</id>
<name>insert_C</name>
<def>
<defstr>An edit to insert a cytidine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>insert C</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000921</id>
<name>insert_dinucleotide</name>
<def>
<defstr>An edit to insert a dinucleotide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>insert dinucleotide</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000922</id>
<name>substitute_C_to_U</name>
<def>
<defstr>An edit to substitute an U for a C.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>substitute C to U</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000923</id>
<name>insert_G</name>
<def>
<defstr>An edit to insert a G.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>insert G</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000924</id>
<name>insert_GC</name>
<def>
<defstr>An edit to insert a GC dinucleotide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.</comment>
<synonym scope="exact">
<synonym_text>insert GC</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000925</id>
<name>insert_GU</name>
<def>
<defstr>An edit to insert a GU dinucleotide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.</comment>
<synonym scope="exact">
<synonym_text>insert GU</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000926</id>
<name>insert_CU</name>
<def>
<defstr>An edit to insert a CU dinucleotide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.</comment>
<synonym scope="exact">
<synonym_text>insert CU</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000927</id>
<name>insert_AU</name>
<def>
<defstr>An edit to insert a AU dinucleotide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.</comment>
<synonym scope="exact">
<synonym_text>insert AU</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000928</id>
<name>insert_AA</name>
<def>
<defstr>An edit to insert a AA dinucleotide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.</comment>
<synonym scope="exact">
<synonym_text>insert AA</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000929</id>
<name>edited_mRNA</name>
<def>
<defstr>An mRNA that is edited.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>edited mRNA</synonym_text>
</synonym>
<is_a>SO:0000873</is_a>
<intersection_of>
<to>SO:0000873</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000116</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000930</id>
<name>guide_RNA_region</name>
<def>
<defstr>A region of guide RNA.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>guide RNA region</synonym_text>
</synonym>
<is_a>SO:0000834</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000602</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000931</id>
<name>anchor_region</name>
<def>
<defstr>A region of a guide_RNA that base-pairs to a target mRNA.</defstr>
<dbxref>
<acc>jk</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>anchor region</synonym_text>
</synonym>
<is_a>SO:0000930</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000932</id>
<name>pre_edited_mRNA</name>
<synonym scope="exact">
<synonym_text>pre-edited mRNA</synonym_text>
</synonym>
<is_a>SO:0000120</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000933</id>
<name>intermediate</name>
<def>
<defstr>An attribute to describe a feature between stages of processing.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000934</id>
<name>miRNA_target_site</name>
<def>
<defstr>A miRNA target site is a binding site where the molecule is a micro RNA.</defstr>
<dbxref>
<acc>cds</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>miRNA target site</synonym_text>
</synonym>
<is_a>SO:0000409</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000935</id>
<name>edited_CDS</name>
<def>
<defstr>A CDS that is edited.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>edited CDS</synonym_text>
</synonym>
<is_a>SO:0000316</is_a>
<intersection_of>
<to>SO:0000316</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000116</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000936</id>
<name>vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment</name>
<synonym scope="exact">
<synonym_text>vertebrate immunoglobulin T cell receptor rearranged segment</synonym_text>
</synonym>
<is_a>SO:0000301</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000937</id>
<name>vertebrate_immune_system_feature</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000938</id>
<name>vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster</name>
<synonym scope="exact">
<synonym_text>vertebrate immunoglobulin T cell receptor rearranged gene cluster</synonym_text>
</synonym>
<is_a>SO:0000301</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000939</id>
<name>vertebrate_immune_system_gene_recombination_signal_feature</name>
<synonym scope="exact">
<synonym_text>vertebrate immune system gene recombination signal feature</synonym_text>
</synonym>
<is_a>SO:0000301</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000940</id>
<name>recombinationally_rearranged</name>
<synonym scope="exact">
<synonym_text>recombinationally rearranged</synonym_text>
</synonym>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000941</id>
<name>recombinationally_rearranged_vertebrate_immune_system_gene</name>
<def>
<defstr>A recombinationally rearranged gene of the vertebrate immune system.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>recombinationally rearranged vertebrate immune system gene</synonym_text>
</synonym>
<is_a>SO:0000456</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000942</id>
<name>attP_site</name>
<def>
<defstr>An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>attP site</synonym_text>
</synonym>
<is_a>SO:0000946</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0001042</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000943</id>
<name>attB_site</name>
<def>
<defstr>An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>attB site</synonym_text>
</synonym>
<is_a>SO:0000946</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000944</id>
<name>attL_site</name>
<def>
<defstr>A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>attBP'</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>attL site</synonym_text>
</synonym>
<is_a>SO:0000946</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000945</id>
<name>attR_site</name>
<def>
<defstr>A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>attPB'</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>attR site</synonym_text>
</synonym>
<is_a>SO:0000946</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000946</id>
<name>integration_excision_site</name>
<def>
<defstr>A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>attachment site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>integration excision site</synonym_text>
</synonym>
<is_a>SO:0000342</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000947</id>
<name>resolution_site</name>
<def>
<defstr>A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>res site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>resolution site</synonym_text>
</synonym>
<is_a>SO:0000342</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000948</id>
<name>inversion_site</name>
<def>
<defstr>A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.</comment>
<synonym scope="exact">
<synonym_text>inversion site</synonym_text>
</synonym>
<is_a>SO:0000342</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000949</id>
<name>dif_site</name>
<def>
<defstr>A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>dif site</synonym_text>
</synonym>
<is_a>SO:0000947</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000950</id>
<name>attC_site</name>
<def>
<defstr>An attC site is a sequence required for the integration of a DNA of an integron.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>attC site</synonym_text>
</synonym>
<is_a>SO:0000946</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000365</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000951</id>
<name>eukaryotic_terminator</name>
<synonym scope="exact">
<synonym_text>eukaryotic terminator</synonym_text>
</synonym>
<is_a>SO:0000141</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000952</id>
<name>oriV</name>
<def>
<defstr>An origin of vegetative replication in plasmids and phages.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>origin of vegetative replication</synonym_text>
</synonym>
<is_a>SO:0000296</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000953</id>
<name>oriC</name>
<def>
<defstr>An origin of bacterial chromosome replication.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>origin of bacterial chromosome replication</synonym_text>
</synonym>
<is_a>SO:0000296</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000954</id>
<name>DNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, DNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>DNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000352</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000955</id>
<name>double_stranded_DNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, double-stranded DNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>double stranded DNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000954</is_a>
<intersection_of>
<to>SO:0000954</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000985</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000956</id>
<name>single_stranded_DNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, single-stranded DNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>single stranded DNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000954</is_a>
<intersection_of>
<to>SO:0000954</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000984</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000957</id>
<name>linear_double_stranded_DNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, double-stranded, linear DNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>linear double stranded DNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000955</is_a>
<intersection_of>
<to>SO:0000955</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000987</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000958</id>
<name>circular_double_stranded_DNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>circular double stranded DNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000955</is_a>
<intersection_of>
<to>SO:0000955</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000988</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000959</id>
<name>linear_single_stranded_DNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>linear single stranded DNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000956</is_a>
<intersection_of>
<to>SO:0000956</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000987</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000960</id>
<name>circular_single_stranded_DNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>circular single stranded DNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000956</is_a>
<intersection_of>
<to>SO:0000956</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000988</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000961</id>
<name>RNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, RNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>RNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000356</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000962</id>
<name>single_stranded_RNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, single-stranded RNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>single stranded RNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000961</is_a>
<intersection_of>
<to>SO:0000961</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000984</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000963</id>
<name>linear_single_stranded_RNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, single-stranded, linear RNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>linear single stranded RNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000962</is_a>
<intersection_of>
<to>SO:0000962</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000987</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000964</id>
<name>linear_double_stranded_RNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, double-stranded, linear RNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>linear double stranded RNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000965</is_a>
<intersection_of>
<to>SO:0000965</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000987</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000965</id>
<name>double_stranded_RNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, double-stranded RNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>double stranded RNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000961</is_a>
<intersection_of>
<to>SO:0000961</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000985</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000966</id>
<name>circular_single_stranded_RNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>circular single stranded RNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000962</is_a>
<intersection_of>
<to>SO:0000962</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000988</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000967</id>
<name>circular_double_stranded_RNA_chromosome</name>
<def>
<defstr>Structural unit composed of a self-replicating, double-stranded, circular RNA molecule.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>circular double stranded RNA chromosome</synonym_text>
</synonym>
<is_a>SO:0000965</is_a>
<intersection_of>
<to>SO:0000965</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000988</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000968</id>
<name>sequence_replication_mode</name>
<comment>This has been obsoleted as it represents a process. replaced_by: GO:0034961.</comment>
<synonym scope="exact">
<synonym_text>sequence replication mode</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000969</id>
<name>rolling_circle</name>
<comment>This has been obsoleted as it represents a process. replaced_by: GO:0070581.</comment>
<synonym scope="exact">
<synonym_text>rolling circle</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Rolling_circle</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000970</id>
<name>theta_replication</name>
<comment>This has been obsoleted as it represents a process. replaced_by: GO:0070582</comment>
<synonym scope="exact">
<synonym_text>theta replication</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000971</id>
<name>DNA_replication_mode</name>
<comment>This has been obsoleted as it represents a process. replaced_by: GO:0006260.</comment>
<synonym scope="exact">
<synonym_text>DNA replication mode</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000972</id>
<name>RNA_replication_mode</name>
<comment>This has been obsoleted as it represents a process. replaced_by: GO:0034961.</comment>
<synonym scope="exact">
<synonym_text>RNA replication mode</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000973</id>
<name>insertion_sequence</name>
<def>
<defstr>A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.</defstr>
<dbxref>
<acc>as</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>insertion sequence</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>IS</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Insertion_sequence</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000208</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000975</id>
<name>minicircle_gene</name>
<synonym scope="exact">
<synonym_text>minicircle gene</synonym_text>
</synonym>
<is_a>SO:0000089</is_a>
<intersection_of>
<to>SO:0000089</to>
</intersection_of>
<intersection_of>
<type>OBO_REL:part_of</type>
<to>SO:0000980</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000976</id>
<name>cryptic</name>
<def>
<defstr>A feature_attribute describing a feature that is not manifest under normal conditions.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000977</id>
<name>anchor_binding_site</name>
<comment>Part of an edited transcript only.</comment>
<synonym scope="exact">
<synonym_text>anchor binding site</synonym_text>
</synonym>
<is_a>SO:0000833</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000978</id>
<name>template_region</name>
<def>
<defstr>A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.</defstr>
<dbxref>
<acc>jk</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>information region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>template region</synonym_text>
</synonym>
<is_a>SO:0000930</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000979</id>
<name>gRNA_encoding</name>
<def>
<defstr>A non-protein_coding gene that encodes a guide_RNA.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gRNA encoding</synonym_text>
</synonym>
<is_a>SO:0000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000980</id>
<name>minicircle</name>
<alt_id>SO:0000974</alt_id>
<def>
<defstr>A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs.</defstr>
<dbxref>
<acc>8395055</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>minicircle_chromosome</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Minicircle</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000741</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000981</id>
<name>rho_dependent_bacterial_terminator</name>
<synonym scope="exact">
<synonym_text>rho dependent bacterial terminator</synonym_text>
</synonym>
<is_a>SO:0000614</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000982</id>
<name>rho_independent_bacterial_terminator</name>
<synonym scope="exact">
<synonym_text>rho independent bacterial terminator</synonym_text>
</synonym>
<is_a>SO:0000614</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000983</id>
<name>strand_attribute</name>
<comment>Attributes added to describe the different kinds of replicon. SO workshop, September 2006.</comment>
<synonym scope="exact">
<synonym_text>strand attribute</synonym_text>
</synonym>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000984</id>
<name>single</name>
<comment>Attributes added to describe the different kinds of replicon. SO workshop, September 2006.</comment>
<is_a>SO:0000983</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000985</id>
<name>double</name>
<comment>Attributes added to describe the different kinds of replicon. SO workshop, September 2006.</comment>
<is_a>SO:0000983</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000986</id>
<name>topology_attribute</name>
<comment>Attributes added to describe the different kinds of replicon. SO workshop, September 2006.</comment>
<synonym scope="exact">
<synonym_text>topology attribute</synonym_text>
</synonym>
<is_a>SO:0000443</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000987</id>
<name>linear</name>
<def>
<defstr>A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Attributes added to describe the different kinds of replicon. SO workshop, September 2006.</comment>
<synonym scope="related">
<synonym_text>two-ended</synonym_text>
</synonym>
<is_a>SO:0000986</is_a>
<disjoint_from>SO:0000988</disjoint_from>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000988</id>
<name>circular</name>
<def>
<defstr>A quality of a nucleotide polymer that has no terminal nucleotide residues.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Attributes added to describe the different kinds of replicon. SO workshop, September 2006.</comment>
<synonym scope="related">
<synonym_text>zero-ended</synonym_text>
</synonym>
<is_a>SO:0000986</is_a>
<disjoint_from>SO:0000987</disjoint_from>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000989</id>
<name>class_II_RNA</name>
<def>
<defstr>Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.</defstr>
<dbxref>
<acc>15333696</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>class II RNA</synonym_text>
</synonym>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000990</id>
<name>class_I_RNA</name>
<def>
<defstr>Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.</defstr>
<dbxref>
<acc>15333696</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.</comment>
<synonym scope="exact">
<synonym_text>class I RNA</synonym_text>
</synonym>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000991</id>
<name>genomic_DNA</name>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>genomic DNA</synonym_text>
</synonym>
<is_a>SO:0000352</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000992</id>
<name>BAC_cloned_genomic_insert</name>
<comment>Requested by Andy Schroder - Flybase Harvard, Nov 2006.</comment>
<synonym scope="exact">
<synonym_text>BAC cloned genomic insert</synonym_text>
</synonym>
<is_a>SO:0000914</is_a>
<intersection_of>
<to>SO:0000914</to>
</intersection_of>
<intersection_of>
<type>derives_from</type>
<to>SO:0000153</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000993</id>
<name>consensus</name>
<comment>Term added Dec 06 to comply with mapping to MGED terms.It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.</comment>
<is_a>SO:0000905</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000994</id>
<name>consensus_region</name>
<comment>DO not obsolete without considering MGED mapping.</comment>
<synonym scope="exact">
<synonym_text>consensus region</synonym_text>
</synonym>
<is_a>SO:0001410</is_a>
<intersection_of>
<to>SO:0000001</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000993</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000995</id>
<name>consensus_mRNA</name>
<comment>DO not obsolete without considering MGED mapping.</comment>
<synonym scope="exact">
<synonym_text>consensus mRNA</synonym_text>
</synonym>
<is_a>SO:0000234</is_a>
<is_a>SO:0000994</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000993</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000996</id>
<name>predicted_gene</name>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>predicted gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000732</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000997</id>
<name>gene_fragment</name>
<comment>This term is mapped to MGED. Do not obsolete without consulting MGED ontology.</comment>
<synonym scope="exact">
<synonym_text>gene fragment</synonym_text>
</synonym>
<is_a>SO:0000842</is_a>
<intersection_of>
<to>SO:0000842</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000731</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000998</id>
<name>recursive_splice_site</name>
<def>
<defstr>A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons.</defstr>
<dbxref>
<acc>http://www.genetics.org/cgi/content/full/170/2/661</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>recursive splice site</synonym_text>
</synonym>
<is_a>SO:0001419</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0000999</id>
<name>BAC_end</name>
<def>
<defstr>A region of sequence from the end of a BAC clone that may provide a highly specific marker.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Requested by Keith Boroevich December, 2006.</comment>
<synonym scope="exact">
<synonym_text>BAC end</synonym_text>
</synonym>
<is_a>SO:0000150</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000153</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001000</id>
<name>rRNA_16S</name>
<def>
<defstr>A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>16S ribosomal RNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>16S rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>16S SSU RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rRNA 16S</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/16S_ribosomal_RNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000650</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001001</id>
<name>rRNA_23S</name>
<def>
<defstr>A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>23S LSU rRNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>23S ribosomal RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>23S rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rRNA 23S</synonym_text>
</synonym>
<is_a>SO:0000651</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001002</id>
<name>rRNA_25S</name>
<def>
<defstr>A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>25S LSU rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>25S ribosomal RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>25S rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rRNA 25S</synonym_text>
</synonym>
<is_a>SO:0000651</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001003</id>
<name>solo_LTR</name>
<def>
<defstr>A recombination product between the 2 LTR of the same element.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Requested by Hadi Quesneville January 2007.</comment>
<synonym scope="exact">
<synonym_text>solo LTR</synonym_text>
</synonym>
<is_a>SO:0000286</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001004</id>
<name>low_complexity</name>
<synonym scope="exact">
<synonym_text>low complexity</synonym_text>
</synonym>
<is_a>SO:0000905</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001005</id>
<name>low_complexity_region</name>
<synonym scope="exact">
<synonym_text>low complexity region</synonym_text>
</synonym>
<is_a>SO:0001410</is_a>
<intersection_of>
<to>SO:0000001</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001004</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001006</id>
<name>prophage</name>
<def>
<defstr>A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island".</defstr>
<dbxref>
<acc>jl</acc>
<dbname>GOC</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Prophage</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000113</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001007</id>
<name>cryptic_prophage</name>
<def>
<defstr>A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.</defstr>
<dbxref>
<acc>jl</acc>
<dbname>GOC</dbname>
</dbxref>
</def>
<comment>This is not cryptic in the same sense as a cryptic gene or cryptic splice site.</comment>
<synonym scope="exact">
<synonym_text>cryptic prophage</synonym_text>
</synonym>
<xref_analog>
<acc>http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w%20dbxref</acc>
<dbname>URL</dbname>
</xref_analog>
<is_a>SO:0000772</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001008</id>
<name>tetraloop</name>
<def>
<defstr>A base-paired stem with loop of 4 non-hydrogen bonded nucleotides.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Tetraloop</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000313</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001009</id>
<name>DNA_constraint_sequence</name>
<def>
<defstr>A double-stranded DNA used to control macromolecular structure and function.</defstr>
</def>
<synonym scope="exact">
<synonym_text>DNA constraint</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DNA constraint sequence</synonym_text>
</synonym>
<is_a>SO:0000442</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001010</id>
<name>i_motif</name>
<def>
<defstr>A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.</defstr>
<dbxref>
<acc>9753739</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>i motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>short intercalated motif</synonym_text>
</synonym>
<is_a>SO:0000142</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001011</id>
<name>PNA_oligo</name>
<def>
<defstr>Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>peptide nucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>PNA oligo</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Peptide_nucleic_acid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001247</is_a>
<intersection_of>
<to>SO:0001247</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001184</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001012</id>
<name>DNAzyme</name>
<def>
<defstr>A DNA sequence with catalytic activity.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Added by request from Colin Batchelor.</comment>
<synonym scope="exact">
<synonym_text>catalytic DNA</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>deoxyribozyme</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DNA enzyme</synonym_text>
</synonym>
<is_a>SO:0000696</is_a>
<intersection_of>
<to>SO:0000696</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001185</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001013</id>
<name>MNP</name>
<def>
<defstr>A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>multiple nucleotide polymorphism</synonym_text>
</synonym>
<is_a>SO:1000002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001014</id>
<name>intron_domain</name>
<comment>Requested by Colin Batchelor, Feb 2007.</comment>
<synonym scope="exact">
<synonym_text>intron domain</synonym_text>
</synonym>
<is_a>SO:0000835</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000188</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001015</id>
<name>wobble_base_pair</name>
<def>
<defstr>A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C.</defstr>
<dbxref>
<acc>11256617</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>wobble base pair</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>wobble pair</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Wobble_base_pair</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000028</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001016</id>
<name>internal_guide_sequence</name>
<def>
<defstr>A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>IGS</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>internal guide sequence</synonym_text>
</synonym>
<is_a>SO:0001014</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000587</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001017</id>
<name>silent_mutation</name>
<comment>Added in March 2007 in after meeting with pharmgkb.</comment>
<synonym scope="exact">
<synonym_text>silent mutation</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Silent_mutation</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:1000132</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001018</id>
<name>epitope</name>
<def>
<defstr>A region of a macromolecule that is recognized by the immune system.</defstr>
<dbxref>
<acc>http://en.wikipedia.org/wiki/Epitope</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Requested by Trish Whetzel.</comment>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Epitope</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000409</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001019</id>
<name>copy_number_variation</name>
<def>
<defstr>A variation that increases or decreases the copy number of a given region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CNP</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>CNV</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>copy number polymorphism</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>copy number variation</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Copy_number_variation</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001060</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001020</id>
<name>sequence_variant_affecting_copy_number</name>
<synonym scope="exact">
<synonym_text>mutation affecting copy number</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting copy number</synonym_text>
</synonym>
<is_a>SO:1000132</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001021</id>
<name>chromosome_breakpoint</name>
<alt_id>SO:0001242</alt_id>
<synonym scope="exact">
<synonym_text>aberration breakpoint</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>aberration_junction</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>chromosome breakpoint</synonym_text>
</synonym>
<is_a>SO:0000699</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000340</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001022</id>
<name>inversion_breakpoint</name>
<def>
<defstr>The point within a chromosome where an inversion begins or ends.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>inversion breakpoint</synonym_text>
</synonym>
<is_a>SO:0001021</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001023</id>
<name>allele</name>
<def>
<defstr>An allele is one of a set of coexisting sequence variants of a gene.</defstr>
<dbxref>
<acc>immuno_workshop</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>allelomorph</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Allele</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001060</is_a>
<relationship>
<type>variant_of</type>
<to>SO:0000704</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001024</id>
<name>haplotype</name>
<def>
<defstr>A haplotype is one of a set of coexisting sequence variants of a haplotype block.</defstr>
<dbxref>
<acc>immuno_workshop</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Haplotype</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001060</is_a>
<relationship>
<type>variant_of</type>
<to>SO:0000355</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001025</id>
<name>polymorphic_sequence_variant</name>
<def>
<defstr>A sequence variant that is segregating in one or more natural populations of a species.</defstr>
<dbxref>
<acc>immuno_workshop</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>polymorphic sequence variant</synonym_text>
</synonym>
<is_a>SO:0001060</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001026</id>
<name>genome</name>
<def>
<defstr>A genome is the sum of genetic material within a cell or virion.</defstr>
<dbxref>
<acc>immuno_workshop</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Genome</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001260</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001027</id>
<name>genotype</name>
<def>
<defstr>A genotype is a variant genome, complete or incomplete.</defstr>
<dbxref>
<acc>immuno_workshop</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Genotype</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001060</is_a>
<relationship>
<type>variant_of</type>
<to>SO:0001026</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001028</id>
<name>diplotype</name>
<def>
<defstr>A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.</defstr>
<dbxref>
<acc>immuno_workshop</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0001060</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001029</id>
<name>direction_attribute</name>
<synonym scope="exact">
<synonym_text>direction attribute</synonym_text>
</synonym>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001030</id>
<name>forward</name>
<def>
<defstr>Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0001029</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001031</id>
<name>reverse</name>
<def>
<defstr>Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0001029</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001032</id>
<name>mitochondrial_DNA</name>
<comment>This terms is used by MO.</comment>
<synonym scope="exact">
<synonym_text>mitochondrial DNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Mitochondrial_DNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000737</is_a>
<intersection_of>
<to>SO:0000737</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000352</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001033</id>
<name>chloroplast_DNA</name>
<comment>This term is used by MO.</comment>
<synonym scope="exact">
<synonym_text>chloroplast DNA</synonym_text>
</synonym>
<is_a>SO:0000745</is_a>
<intersection_of>
<to>SO:0000745</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000352</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001034</id>
<name>mirtron</name>
<def>
<defstr>A debranched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.</defstr>
<dbxref>
<acc>17589500</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Ruby et al. Nature 448:83 desribe a new class of miRNAs that are derived from debranched introns.</comment>
<is_a>SO:0001014</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001035</id>
<name>piRNA</name>
<def>
<defstr>A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>piwi-associated RNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/PiRNA</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001036</id>
<name>arginyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>arginyl tRNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000212</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001037</id>
<name>mobile_genetic_element</name>
<def>
<defstr>A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome.</defstr>
<dbxref>
<acc>14681355</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>MGE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>mobile genetic element</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Mobile_genetic_element</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<intersection_of>
<to>SO:0000001</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001234</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001038</id>
<name>extrachromosomal_mobile_genetic_element</name>
<def>
<defstr>An MGE that is not integrated into the host chromosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>extrachromosomal mobile genetic element</synonym_text>
</synonym>
<is_a>SO:0001037</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001039</id>
<name>integrated_mobile_genetic_element</name>
<def>
<defstr>An MGE that is integrated into the host chromosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>integrated mobile genetic element</synonym_text>
</synonym>
<is_a>SO:0001037</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001040</id>
<name>integrated_plasmid</name>
<def>
<defstr>A plasmid sequence that is integrated within the host chromosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>integrated plasmid</synonym_text>
</synonym>
<is_a>SO:0001039</is_a>
<intersection_of>
<to>SO:0001039</to>
</intersection_of>
<intersection_of>
<type>derives_from</type>
<to>SO:0000155</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001041</id>
<name>viral_sequence</name>
<def>
<defstr>The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.</comment>
<synonym scope="exact">
<synonym_text>viral sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>virus sequence</synonym_text>
</synonym>
<is_a>SO:0001038</is_a>
<is_a>SO:0001235</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001042</id>
<name>phage_sequence</name>
<def>
<defstr>The nucleotide sequence of a virus that infects bacteria.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>bacteriophage</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>phage</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>phage sequence</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Bacteriophage</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001041</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001043</id>
<name>attCtn_site</name>
<def>
<defstr>An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.</defstr>
<dbxref>
<acc>at</acc>
<dbname>Phigo</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>attCtn site</synonym_text>
</synonym>
<is_a>SO:0000946</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000371</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001044</id>
<name>nuclear_mt_pseudogene</name>
<def>
<defstr>A nuclear pseudogene of a mitochndrial gene.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>nuclear mitochondrial pseudogene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nuclear mt pseudogene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>NUMT</synonym_text>
</synonym>
<is_a>SO:0000336</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001045</id>
<name>cointegrated_plasmid</name>
<def>
<defstr>A MGE region consisting of two fused plasmids resulting from a replicative transposition event.</defstr>
<dbxref>
<acc>at</acc>
<dbname>phigo</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cointegrated plasmid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>cointegrated replicon</synonym_text>
</synonym>
<is_a>SO:0001039</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001046</id>
<name>IRLinv_site</name>
<def>
<defstr>Component of the inversion site located at the left of a region susceptible to site-specific inversion.</defstr>
<dbxref>
<acc>at</acc>
<dbname>Phigo</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>IRLinv site</synonym_text>
</synonym>
<is_a>SO:0001048</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000948</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001047</id>
<name>IRRinv_site</name>
<def>
<defstr>Component of the inversion site located at the right of a region susceptible to site-specific inversion.</defstr>
<dbxref>
<acc>at</acc>
<dbname>Phigo</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>IRRinv site</synonym_text>
</synonym>
<is_a>SO:0001048</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000948</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001048</id>
<name>inversion_site_part</name>
<def>
<defstr>A region located within an inversion site.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>A term created to allow the parts of an inversion site have an is_a path back to the root.</comment>
<synonym scope="exact">
<synonym_text>inversion site part</synonym_text>
</synonym>
<is_a>SO:0000342</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001049</id>
<name>defective_conjugative_transposon</name>
<def>
<defstr>An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.</defstr>
<dbxref>
<acc>ariane</acc>
<dbname>Phigo</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>defective conjugative transposon</synonym_text>
</synonym>
<is_a>SO:0000772</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001050</id>
<name>repeat_fragment</name>
<def>
<defstr>A portion of a repeat, interrupted by the insertion of another element.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Requested by Chris Smith, and others at Flybase to help annotate nested repeats.</comment>
<synonym scope="exact">
<synonym_text>repeat fragment</synonym_text>
</synonym>
<is_a>SO:0000657</is_a>
<is_a>SO:0000840</is_a>
<intersection_of>
<to>SO:0000657</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000731</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001051</id>
<name>nested_region</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001052</id>
<name>nested_repeat</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001053</id>
<name>nested_transposon</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001054</id>
<name>transposon_fragment</name>
<synonym scope="exact">
<synonym_text>transposon fragment</synonym_text>
</synonym>
<is_a>SO:0000101</is_a>
<intersection_of>
<to>SO:0000101</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000731</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001055</id>
<name>transcriptional_cis_regulatory_region</name>
<def>
<defstr>A regulatory_region that modulates the transcription of a gene or genes.</defstr>
<dbxref>
<acc>regcreative</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>transcriptional cis regulatory region</synonym_text>
</synonym>
<is_a>SO:0005836</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001056</id>
<name>splicing_regulatory_region</name>
<def>
<defstr>A regulatory_region that modulates splicing.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>splicing regulatory region</synonym_text>
</synonym>
<is_a>SO:0005836</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001057</id>
<name>enhanceosome</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001058</id>
<name>promoter_targeting_sequence</name>
<def>
<defstr>A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.</defstr>
<dbxref>
<acc>regcreative</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>promoter targeting sequence</synonym_text>
</synonym>
<is_a>SO:0001055</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001059</id>
<name>sequence_alteration</name>
<alt_id>SO:1000004</alt_id>
<alt_id>SO:1000007</alt_id>
<def>
<defstr>A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Merged with partially characterized change in nucleotide sequence.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>partially characterised change in DNA sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>partially_characterised_change_in_DNA_sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence alteration</synonym_text>
</synonym>
<is_a>SO:0000110</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001060</id>
<name>sequence_variant</name>
<def>
<defstr>A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>sequence variant</synonym_text>
</synonym>
<namespace>sequence</namespace>
<is_root>1</is_root>
</term>
<term>
<id>SO:0001061</id>
<name>propeptide_cleavage_site</name>
<alt_id>BS:00063</alt_id>
<def>
<defstr>The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>propeptide cleavage site</synonym_text>
</synonym>
<is_a>SO:0100011</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0001062</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001062</id>
<name>propeptide</name>
<alt_id>BS:00077</alt_id>
<def>
<defstr>Part of a peptide chain which is cleaved off during the formation of the mature protein.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>propep</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Propeptide</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0100011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001063</id>
<name>immature_peptide_region</name>
<alt_id>BS:00129</alt_id>
<def>
<defstr>An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>immature_peptide_region</synonym_text>
</synonym>
<is_a>SO:0000839</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001064</id>
<name>active_peptide</name>
<alt_id>BS:00076</alt_id>
<def>
<defstr>Active peptides are proteins which are biologically active, released from a precursor molecule.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>active peptide</synonym_text>
</synonym>
<synonym scope="broad">
<synonym_text>peptide</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Peptide</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000419</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001066</id>
<name>compositionally_biased_region_of_peptide</name>
<alt_id>BS:00068</alt_id>
<def>
<defstr>Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>compbias</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="related">
<synonym_text>compositional bias</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>compositionally biased</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>compositionally biased region of peptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>compositionally_biased_region</synonym_text>
</synonym>
<is_a>SO:0000839</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001067</id>
<name>polypeptide_motif</name>
<alt_id>BS:00032</alt_id>
<def>
<defstr>A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="broad">
<synonym_text>motif</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide motif</synonym_text>
</synonym>
<is_a>SO:0100021</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001068</id>
<name>polypeptide_repeat</name>
<alt_id>BS:00070</alt_id>
<def>
<defstr>A polypeptide_repeat is a single copy of an internal sequence repetition.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>polypeptide repeat</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>repeat</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<is_a>SO:0100021</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001070</id>
<name>polypeptide_structural_region</name>
<alt_id>BS:00337</alt_id>
<def>
<defstr>Region of polypeptide with a given structural property.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>polypeptide structural region</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>structural_region</synonym_text>
</synonym>
<is_a>SO:0000839</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001071</id>
<name>membrane_structure</name>
<alt_id>BS:00128</alt_id>
<def>
<defstr>Arrangement of the polypeptide with respect to the lipid bilayer.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>membrane_structure</synonym_text>
</synonym>
<is_a>SO:0001070</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001072</id>
<name>extramembrane_polypeptide_region</name>
<alt_id>BS:00154</alt_id>
<def>
<defstr>Polypeptide region that is localized outside of a lipid bilayer.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>extramembrane</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>extramembrane polypeptide region</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>extramembrane_region</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>topo_dom</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<is_a>SO:0001070</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0001071</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001073</id>
<name>cytoplasmic_polypeptide_region</name>
<alt_id>BS:00145</alt_id>
<def>
<defstr>Polypeptide region that is localized inside the cytoplasm.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="exact">
<synonym_text>cytoplasm_location</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>cytoplasmic polypeptide region</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>inside</synonym_text>
</synonym>
<is_a>SO:0001072</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001074</id>
<name>non_cytoplasmic_polypeptide_region</name>
<alt_id>BS:00144</alt_id>
<def>
<defstr>Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This could be inside an organelle within the cell.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>non cytoplasmic polypeptide region</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="exact">
<synonym_text>non_cytoplasm_location</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>outside</synonym_text>
</synonym>
<is_a>SO:0001072</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001075</id>
<name>intramembrane_polypeptide_region</name>
<alt_id>BS:00156</alt_id>
<def>
<defstr>Polypeptide region present in the lipid bilayer.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>intramembrane</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>intramembrane polypeptide region</synonym_text>
</synonym>
<is_a>SO:0001070</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0001071</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001076</id>
<name>membrane_peptide_loop</name>
<alt_id>BS:00155</alt_id>
<def>
<defstr>Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>membrane peptide loop</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>membrane_loop</synonym_text>
</synonym>
<is_a>SO:0001075</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001077</id>
<name>transmembrane_polypeptide_region</name>
<alt_id>BS:00158</alt_id>
<def>
<defstr>Polypeptide region traversing the lipid bilayer.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curator_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>transmem</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>transmembrane</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>transmembrane polypeptide region</synonym_text>
</synonym>
<is_a>SO:0001075</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001078</id>
<name>polypeptide_secondary_structure</name>
<alt_id>BS:00003</alt_id>
<def>
<defstr>A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Biosapien term was secondary_structure.</comment>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>2nary structure</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide secondary structure</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>secondary structure</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>secondary structure region</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>secondary_structure</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Secondary_structure</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001070</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001079</id>
<name>polypeptide_structural_motif</name>
<alt_id>BS:0000338</alt_id>
<def>
<defstr>Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>polypeptide structural motif</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>structural_motif</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Structural_motif</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001070</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001080</id>
<name>coiled_coil</name>
<alt_id>BS:00041</alt_id>
<def>
<defstr>A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>coiled</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>coiled coil</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Coiled_coil</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001079</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001081</id>
<name>helix_turn_helix</name>
<alt_id>BS:00147</alt_id>
<def>
<defstr>A motif comprising two helices separated by a turn.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>helix turn helix</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>helix-turn-helix</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>HTH</synonym_text>
</synonym>
<is_a>SO:0001079</is_a>
<relationship>
<type>has_part</type>
<to>SO:0001114</to>
</relationship>
<relationship>
<type>has_part</type>
<to>SO:0001128</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001082</id>
<name>polypeptide_sequencing_information</name>
<alt_id>BS:00125</alt_id>
<def>
<defstr>Incompatibility in the sequence due to some experimental problem.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>sequencing_information</synonym_text>
</synonym>
<is_a>SO:0000700</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001083</id>
<name>non_adjacent_residues</name>
<alt_id>BS:00182</alt_id>
<def>
<defstr>Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>non consecutive</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non_cons</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<is_a>SO:0001082</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001084</id>
<name>non_terminal_residue</name>
<alt_id>BS:00072</alt_id>
<def>
<defstr>The residue at an extremity of the sequence is not the terminal residue.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>non terminal</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non_ter</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<is_a>SO:0001082</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001085</id>
<name>sequence_conflict</name>
<alt_id>BS:00069</alt_id>
<def>
<defstr>Different sources report differing sequences.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>conflict</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<is_a>SO:0001082</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001086</id>
<name>sequence_uncertainty</name>
<alt_id>BS:00181</alt_id>
<def>
<defstr>Describes the positions in a sequence where the authors are unsure about the sequence assignment.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>unsure</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<is_a>SO:0001082</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001087</id>
<name>cross_link</name>
<alt_id>BS:00178</alt_id>
<def>
<defstr>Posttranslationally formed amino acid bonds.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>cross_link</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>crosslink</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001088</id>
<name>disulfide_bond</name>
<alt_id>BS:00028</alt_id>
<def>
<defstr>The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>2 discreet & joined.</comment>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>disulfid</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>disulfide</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>disulfide bond</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>disulfide_bond</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>disulphide</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>disulphide bond</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001089</id>
<name>post_translationally_modified_region</name>
<alt_id>BS:00052</alt_id>
<def>
<defstr>A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>mod_res</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>modified residue</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>post_translational_modification</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Post_translational_modification</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0100001</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001090</id>
<name>covalent_binding_site</name>
<alt_id>BS:00246</alt_id>
<def>
<defstr>Binding involving a covalent bond.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>covalent_binding_site</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001091</id>
<name>non_covalent_binding_site</name>
<alt_id>BS:00029</alt_id>
<def>
<defstr>Binding site for any chemical group (co-enzyme, prosthetic group, etc.).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>binding</synonym_text>
<dbxref>
<acc>curation</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="related">
<synonym_text>binding site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non_covalent_binding_site</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001092</id>
<name>polypeptide_metal_contact</name>
<alt_id>BS:00027</alt_id>
<def>
<defstr>Residue is part of a binding site for a metal ion.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>metal_binding</synonym_text>
</synonym>
<is_a>SO:0000409</is_a>
<is_a>SO:0100002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001093</id>
<name>protein_protein_contact</name>
<alt_id>BS:00131</alt_id>
<def>
<defstr>Residues involved in protein-protein interactions.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>Curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>protein protein contact</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>protein protein contact site</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>protein_protein_interaction</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Protein_protein_interaction</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000409</is_a>
<is_a>SO:0100002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001094</id>
<name>polypeptide_calcium_ion_contact_site</name>
<alt_id>BS:00186</alt_id>
<def>
<defstr>Residue involved in contact with calcium.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>ca bind</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Ca_contact_site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide calcium ion contact site</synonym_text>
</synonym>
<is_a>SO:0001092</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001095</id>
<name>polypeptide_cobalt_ion_contact_site</name>
<alt_id>BS:00136</alt_id>
<def>
<defstr>Residue involved in contact with cobalt.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>Co_contact_site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide cobalt ion contact site</synonym_text>
</synonym>
<is_a>SO:0001092</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001096</id>
<name>polypeptide_copper_ion_contact_site</name>
<alt_id>BS:00146</alt_id>
<def>
<defstr>Residue involved in contact with copper.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>Cu_contact_site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide copper ion contact site</synonym_text>
</synonym>
<is_a>SO:0001092</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001097</id>
<name>polypeptide_iron_ion_contact_site</name>
<alt_id>BS:00137</alt_id>
<def>
<defstr>Residue involved in contact with iron.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>Fe_contact_site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide iron ion contact site</synonym_text>
</synonym>
<is_a>SO:0001092</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001098</id>
<name>polypeptide_magnesium_ion_contact_site</name>
<alt_id>BS:00187</alt_id>
<def>
<defstr>Residue involved in contact with magnesium.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>Mg_contact_site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide magnesium ion contact site</synonym_text>
</synonym>
<is_a>SO:0001092</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001099</id>
<name>polypeptide_manganese_ion_contact_site</name>
<alt_id>BS:00140</alt_id>
<def>
<defstr>Residue involved in contact with manganese.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>Mn_contact_site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide manganese ion contact site</synonym_text>
</synonym>
<is_a>SO:0001092</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001100</id>
<name>polypeptide_molybdenum_ion_contact_site</name>
<alt_id>BS:00141</alt_id>
<def>
<defstr>Residue involved in contact with molybdenum.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>Mo_contact_site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide molybdenum ion contact site</synonym_text>
</synonym>
<is_a>SO:0001092</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001101</id>
<name>polypeptide_nickel_ion_contact_site</name>
<alt_id>BS:00142</alt_id>
<def>
<defstr>Residue involved in contact with nickel.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>Ni_contact_site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide nickel ion contact site</synonym_text>
</synonym>
<is_a>SO:0001092</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001102</id>
<name>polypeptide_tungsten_ion_contact_site</name>
<alt_id>BS:00143</alt_id>
<def>
<defstr>Residue involved in contact with tungsten.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>polypeptide tungsten ion contact site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>W_contact_site</synonym_text>
</synonym>
<is_a>SO:0001092</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001103</id>
<name>polypeptide_zinc_ion_contact_site</name>
<alt_id>BS:00185</alt_id>
<def>
<defstr>Residue involved in contact with zinc.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>polypeptide zinc ion contact site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Zn_contact_site</synonym_text>
</synonym>
<is_a>SO:0001092</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001104</id>
<name>catalytic_residue</name>
<alt_id>BS:00026</alt_id>
<def>
<defstr>Amino acid involved in the activity of an enzyme.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>act_site</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>active site residue</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>catalytic residue</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0100019</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001105</id>
<name>polypeptide_ligand_contact</name>
<alt_id>BS:00157</alt_id>
<def>
<defstr>Residues which interact with a ligand.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>polypeptide ligand contact</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>protein-ligand interaction</synonym_text>
</synonym>
<is_a>SO:0000409</is_a>
<is_a>SO:0100002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001106</id>
<name>asx_motif</name>
<alt_id>BS:00202</alt_id>
<def>
<defstr>A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>asx motif</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001107</id>
<name>beta_bulge</name>
<alt_id>BS:00208</alt_id>
<def>
<defstr>A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta bulge</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Beta_bulge</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001108</id>
<name>beta_bulge_loop</name>
<alt_id>BS:00209</alt_id>
<def>
<defstr>A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>//www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>Http</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta bulge loop</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001109</id>
<name>beta_bulge_loop_five</name>
<alt_id>BS:00210</alt_id>
<def>
<defstr>A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta bulge loop five</synonym_text>
</synonym>
<is_a>SO:0001108</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001110</id>
<name>beta_bulge_loop_six</name>
<alt_id>BS:00211</alt_id>
<def>
<defstr>A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta bulge loop six</synonym_text>
</synonym>
<is_a>SO:0001108</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001111</id>
<name>beta_strand</name>
<alt_id>BS:00042</alt_id>
<def>
<defstr>A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>strand</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Beta_sheet</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001112</id>
<name>antiparallel_beta_strand</name>
<alt_id>BS:0000341</alt_id>
<def>
<defstr>A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>antiparallel beta strand</synonym_text>
</synonym>
<is_a>SO:0001111</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001113</id>
<name>parallel_beta_strand</name>
<alt_id>BS:00151</alt_id>
<def>
<defstr>A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>parallel beta strand</synonym_text>
</synonym>
<is_a>SO:0001111</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001114</id>
<name>peptide_helix</name>
<alt_id>BS:00152</alt_id>
<def>
<defstr>A helix is a secondary_structure conformation where the peptide backbone forms a coil.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>helix</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001115</id>
<name>left_handed_peptide_helix</name>
<alt_id>BS:00222</alt_id>
<def>
<defstr>A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>helix-l</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>left handed helix</synonym_text>
</synonym>
<is_a>SO:0001114</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001116</id>
<name>right_handed_peptide_helix</name>
<alt_id>BS:0000339</alt_id>
<def>
<defstr>A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>helix</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>right handed helix</synonym_text>
</synonym>
<is_a>SO:0001114</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001117</id>
<name>alpha_helix</name>
<alt_id>BS:00040</alt_id>
<def>
<defstr>The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>a-helix</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>helix</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Alpha_helix</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001116</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001118</id>
<name>pi_helix</name>
<alt_id>BS:00153</alt_id>
<def>
<defstr>The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>pi helix</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Pi_helix</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001116</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001119</id>
<name>three_ten_helix</name>
<alt_id>BS:0000340</alt_id>
<def>
<defstr>The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>3(10) helix</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>3-10 helix</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>310 helix</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three_ten_helix</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/310_helix</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001116</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001120</id>
<name>polypeptide_nest_motif</name>
<alt_id>BS:00223</alt_id>
<def>
<defstr>A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>nest</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nest_motif</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>polypeptide nest motif</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001121</id>
<name>polypeptide_nest_left_right_motif</name>
<alt_id>BS:00224</alt_id>
<def>
<defstr>A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>nest_left_right</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nest_lr</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide nest left right motif</synonym_text>
</synonym>
<is_a>SO:0001120</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001122</id>
<name>polypeptide_nest_right_left_motif</name>
<alt_id>BS:00225</alt_id>
<def>
<defstr>A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>nest_right_left</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>nest_rl</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide nest right left motif</synonym_text>
</synonym>
<is_a>SO:0001120</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001123</id>
<name>schellmann_loop</name>
<alt_id>BS:00226</alt_id>
<def>
<defstr>A motif of six or seven consecutive residues that contains two H-bonds.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>paperclip</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>paperclip loop</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>schellmann_loop</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001124</id>
<name>schellmann_loop_seven</name>
<alt_id>BS:00228</alt_id>
<def>
<defstr>Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>schellmann loop seven</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>seven-residue schellmann loop</synonym_text>
</synonym>
<is_a>SO:0001123</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001125</id>
<name>schellmann_loop_six</name>
<alt_id>BS:00227</alt_id>
<def>
<defstr>Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>schellmann loop six</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>six-residue schellmann loop</synonym_text>
</synonym>
<is_a>SO:0001123</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001126</id>
<name>serine_threonine_motif</name>
<alt_id>BS:00229</alt_id>
<def>
<defstr>A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>serine/threonine motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>st motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>st_motif</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001127</id>
<name>serine_threonine_staple_motif</name>
<alt_id>BS:00230</alt_id>
<def>
<defstr>A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>serine threonine staple motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>st_staple</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001128</id>
<name>polypeptide_turn_motif</name>
<alt_id>BS:00148</alt_id>
<def>
<defstr>A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>turn</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001129</id>
<name>asx_turn_left_handed_type_one</name>
<alt_id>BS:00206</alt_id>
<def>
<defstr>Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>asx turn left handed type one</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>asx_turn_il</synonym_text>
</synonym>
<is_a>SO:0000912</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001130</id>
<name>asx_turn_left_handed_type_two</name>
<alt_id>BS:00204</alt_id>
<def>
<defstr>Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>asx turn left handed type two</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>asx_turn_iil</synonym_text>
</synonym>
<is_a>SO:0000912</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001131</id>
<name>asx_turn_right_handed_type_two</name>
<alt_id>BS:00205</alt_id>
<def>
<defstr>Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>asx turn right handed type two</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>asx_turn_iir</synonym_text>
</synonym>
<is_a>SO:0000912</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001132</id>
<name>asx_turn_right_handed_type_one</name>
<alt_id>BS:00207</alt_id>
<def>
<defstr>Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>asx turn type right handed type one</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>asx_turn_ir</synonym_text>
</synonym>
<is_a>SO:0000912</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001133</id>
<name>beta_turn</name>
<alt_id>BS:00212</alt_id>
<def>
<defstr>A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn</synonym_text>
</synonym>
<is_a>SO:0001128</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001134</id>
<name>beta_turn_left_handed_type_one</name>
<alt_id>BS:00215</alt_id>
<def>
<defstr>Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn left handed type one</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>beta_turn_il</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type I' beta turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type I' turn</synonym_text>
</synonym>
<is_a>SO:0001133</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001135</id>
<name>beta_turn_left_handed_type_two</name>
<alt_id>BS:00213</alt_id>
<def>
<defstr>Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn left handed type two</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>beta_turn_iil</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type II' beta turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type II' turn</synonym_text>
</synonym>
<is_a>SO:0001133</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001136</id>
<name>beta_turn_right_handed_type_one</name>
<alt_id>BS:00216</alt_id>
<def>
<defstr>Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn right handed type one</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>beta_turn_ir</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type I beta turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type I turn</synonym_text>
</synonym>
<is_a>SO:0001133</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001137</id>
<name>beta_turn_right_handed_type_two</name>
<alt_id>BS:00214</alt_id>
<def>
<defstr>Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn right handed type two</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>beta_turn_iir</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type II beta turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type II turn</synonym_text>
</synonym>
<is_a>SO:0001133</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001138</id>
<name>gamma_turn</name>
<alt_id>BS:00219</alt_id>
<def>
<defstr>Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>gamma turn</synonym_text>
</synonym>
<is_a>SO:0001128</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001139</id>
<name>gamma_turn_classic</name>
<alt_id>BS:00220</alt_id>
<def>
<defstr>Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>classic gamma turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>gamma turn classic</synonym_text>
</synonym>
<is_a>SO:0001138</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001140</id>
<name>gamma_turn_inverse</name>
<alt_id>BS:00221</alt_id>
<def>
<defstr>Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>gamma turn inverse</synonym_text>
</synonym>
<is_a>SO:0001138</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001141</id>
<name>serine_threonine_turn</name>
<alt_id>BS:00231</alt_id>
<def>
<defstr>A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>serine/threonine turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>st_turn</synonym_text>
</synonym>
<is_a>SO:0001128</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001142</id>
<name>st_turn_left_handed_type_one</name>
<alt_id>BS:00234</alt_id>
<def>
<defstr>The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>st turn left handed type one</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>st_turn_il</synonym_text>
</synonym>
<is_a>SO:0001141</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001143</id>
<name>st_turn_left_handed_type_two</name>
<alt_id>BS:00232</alt_id>
<def>
<defstr>The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>st turn left handed type two</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>st_turn_iil</synonym_text>
</synonym>
<is_a>SO:0001141</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001144</id>
<name>st_turn_right_handed_type_one</name>
<alt_id>BS:00235</alt_id>
<def>
<defstr>The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>st turn right handed type one</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>st_turn_ir</synonym_text>
</synonym>
<is_a>SO:0001141</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001145</id>
<name>st_turn_right_handed_type_two</name>
<alt_id>BS:00233</alt_id>
<def>
<defstr>The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>st turn right handed type two</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>st_turn_iir</synonym_text>
</synonym>
<is_a>SO:0001141</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001146</id>
<name>polypeptide_variation_site</name>
<alt_id>BS:00336</alt_id>
<def>
<defstr>A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>sequence_variations</synonym_text>
</synonym>
<is_a>SO:0000839</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001147</id>
<name>natural_variant_site</name>
<alt_id>BS:00071</alt_id>
<def>
<defstr>Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<synonym scope="broad">
<synonym_text>natural_variant</synonym_text>
</synonym>
<synonym scope="broad">
<synonym_text>sequence variation</synonym_text>
</synonym>
<synonym scope="broad">
<synonym_text>variant</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<is_a>SO:0001146</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001148</id>
<name>mutated_variant_site</name>
<alt_id>BS:00036</alt_id>
<def>
<defstr>Site which has been experimentally altered.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="exact">
<synonym_text>mutagen</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>mutagenesis</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>mutated_site</synonym_text>
</synonym>
<is_a>SO:0001146</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001149</id>
<name>alternate_sequence_site</name>
<alt_id>BS:00073</alt_id>
<alt_id>SO:0001065</alt_id>
<def>
<defstr>Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>curation_manual</acc>
<dbname>UniProt</dbname>
</dbxref>
</def>
<comment>Discrete.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>alternative_sequence</synonym_text>
</synonym>
<synonym scope="narrow">
<synonym_text>isoform</synonym_text>
</synonym>
<synonym scope="narrow">
<synonym_text>sequence variation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>var_seq</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="narrow">
<synonym_text>varsplic</synonym_text>
</synonym>
<is_a>SO:0001146</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001150</id>
<name>beta_turn_type_six</name>
<def>
<defstr>A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn type six</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>cis-proline loop</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VI beta turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VI turn</synonym_text>
</synonym>
<is_a>SO:0001133</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001151</id>
<name>beta_turn_type_six_a</name>
<def>
<defstr>A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.</defstr>
<dbxref>
<acc>2371257</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn type six a</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VIa beta turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VIa turn</synonym_text>
</synonym>
<is_a>SO:0001150</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001152</id>
<name>beta_turn_type_six_a_one</name>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn type six a one</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VIa1 beta turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VIa1 turn</synonym_text>
</synonym>
<is_a>SO:0001151</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001153</id>
<name>beta_turn_type_six_a_two</name>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn type six a two</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VIa2 beta turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VIa2 turn</synonym_text>
</synonym>
<is_a>SO:0001151</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001154</id>
<name>beta_turn_type_six_b</name>
<def>
<defstr>A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.</defstr>
<dbxref>
<acc>2371257</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn type six b</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VIb beta turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VIb turn</synonym_text>
</synonym>
<is_a>SO:0001150</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001155</id>
<name>beta_turn_type_eight</name>
<def>
<defstr>A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.</defstr>
<dbxref>
<acc>2371257</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>beta turn type eight</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VIII beta turn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>type VIII turn</synonym_text>
</synonym>
<is_a>SO:0001133</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001156</id>
<name>DRE_motif</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.</defstr>
<dbxref>
<acc>12537576</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.</comment>
<synonym scope="exact">
<synonym_text>DRE motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>NDM4</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>WATCGATW_motif</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001157</id>
<name>DMv4_motif</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).</defstr>
<dbxref>
<acc>16827941:12537576</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>directional motif v4</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMv4</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMv4 motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>motif 1 element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>promoter motif 1</synonym_text>
</synonym>
<synonym scope="narrow">
<synonym_text>YGGTCACATR</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001158</id>
<name>E_box_motif</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).</defstr>
<dbxref>
<acc>12537576:16827941</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="narrow">
<synonym_text>AWCAGCTGWT</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>E box motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>generic E box motif</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>NDM5</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001159</id>
<name>DMv5_motif</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).</defstr>
<dbxref>
<acc>12537576:16827941</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>directional motif v5</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMv5</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMv5 motif</synonym_text>
</synonym>
<synonym scope="narrow">
<synonym_text>KTYRGTATWTTT</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>promoter motif 6</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001160</id>
<name>DMv3_motif</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).</defstr>
<dbxref>
<acc>12537576:16827941</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>directional motif v3</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMv3</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMv3 motif</synonym_text>
</synonym>
<synonym scope="narrow">
<synonym_text>KNNCAKCNCTRNY</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>promoter motif 7</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001161</id>
<name>DMv2_motif</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).</defstr>
<dbxref>
<acc>12537576:16827941</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>directional motif v2</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMv2</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMv2 motif</synonym_text>
</synonym>
<synonym scope="narrow">
<synonym_text>MKSYGGCARCGSYSS</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>promoter motif 8</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001162</id>
<name>MTE</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).</defstr>
<dbxref>
<acc>12537576:15231738</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="narrow">
<synonym_text>CSARCSSAACGS</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>motif ten element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>motif_ten_element</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001163</id>
<name>INR1_motif</name>
<def>
<defstr>A promoter motif with consensus sequence TCATTCG.</defstr>
<dbxref>
<acc>16827941</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>directional motif p3</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>directional promoter motif 3</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMp3</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>INR1 motif</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001164</id>
<name>DPE1_motif</name>
<def>
<defstr>A promoter motif with consensus sequence CGGACGT.</defstr>
<dbxref>
<acc>16827941</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>directional motif 5</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>directional promoter motif 5</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMp5</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DPE1 motif</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001165</id>
<name>DMv1_motif</name>
<def>
<defstr>A promoter motif with consensus sequence CARCCCT.</defstr>
<dbxref>
<acc>16827941</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>directional promoter motif v1</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>DMv1</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DMv1 motif</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001166</id>
<name>GAGA_motif</name>
<def>
<defstr>A non directional promoter motif with consensus sequence GAGAGCG.</defstr>
<dbxref>
<acc>16827941</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>GAGA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>GAGA motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>NDM1</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001167</id>
<name>NDM2_motif</name>
<def>
<defstr>A non directional promoter motif with consensus CGMYGYCR.</defstr>
<dbxref>
<acc>16827941</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>NDM2</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>NDM2 motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non directional promoter motif 2</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001168</id>
<name>NDM3_motif</name>
<def>
<defstr>A non directional promoter motif with consensus sequence GAAAGCT.</defstr>
<dbxref>
<acc>16827941</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>NDM3</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>NDM3 motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non directional motif 3</synonym_text>
</synonym>
<is_a>SO:0000713</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001169</id>
<name>ds_RNA_viral_sequence</name>
<def>
<defstr>A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>double stranded RNA virus sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ds RNA viral sequence</synonym_text>
</synonym>
<is_a>SO:0001041</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001170</id>
<name>polinton</name>
<def>
<defstr>A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.</defstr>
<dbxref>
<acc>16537396</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>maverick element</synonym_text>
</synonym>
<is_a>SO:0000208</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001171</id>
<name>rRNA_21S</name>
<def>
<defstr>A component of the large ribosomal subunit in mitochondrial rRNA.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>21S LSU rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>21S ribosomal RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>21S rRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>rRNA 21S</synonym_text>
</synonym>
<is_a>SO:0000651</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001172</id>
<name>tRNA_region</name>
<def>
<defstr>A region of a tRNA.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>tRNA region</synonym_text>
</synonym>
<is_a>SO:0000834</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000253</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001173</id>
<name>anticodon_loop</name>
<def>
<defstr>A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.</defstr>
<dbxref>
<acc>0716719207</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>anti-codon loop</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>anticodon loop</synonym_text>
</synonym>
<is_a>SO:0001172</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001174</id>
<name>anticodon</name>
<def>
<defstr>A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>anti-codon</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Anticodon</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001172</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0001173</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001175</id>
<name>CCA_tail</name>
<def>
<defstr>Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.</defstr>
<dbxref>
<acc>0716719207</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CCA sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>CCA tail</synonym_text>
</synonym>
<is_a>SO:0001172</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001176</id>
<name>DHU_loop</name>
<def>
<defstr>Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.</defstr>
<dbxref>
<acc>071671920</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>D loop</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>DHU loop</synonym_text>
</synonym>
<is_a>SO:0001172</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001177</id>
<name>T_loop</name>
<def>
<defstr>Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.</defstr>
<dbxref>
<acc>0716719207</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>T loop</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>TpsiC loop</synonym_text>
</synonym>
<is_a>SO:0001172</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001178</id>
<name>pyrrolysine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding pyrrolysyl tRNA (SO:0000766).</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>pyrrolysine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001179</id>
<name>U3_snoRNA</name>
<def>
<defstr>U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>The definition is most of the old definition for snoRNA (SO:0000275).</comment>
<synonym scope="exact">
<synonym_text>small nucleolar RNA U3</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>snoRNA U3</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U3 small nucleolar RNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U3 snoRNA</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000593</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001180</id>
<name>AU_rich_element</name>
<def>
<defstr>A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.</defstr>
<dbxref>
<acc>7892223</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>ARE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>AU rich element</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>AU-rich element</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/AU-rich_element</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000837</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000205</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001181</id>
<name>Bruno_response_element</name>
<def>
<defstr>A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.</defstr>
<dbxref>
<acc>10893231</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.</comment>
<synonym scope="related">
<synonym_text>BRE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Bruno response element</synonym_text>
</synonym>
<is_a>SO:0000837</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000205</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001182</id>
<name>iron_responsive_element</name>
<def>
<defstr>A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.</defstr>
<dbxref>
<acc>3198610</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>8710843</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>IRE</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>iron responsive element</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Iron_responsive_element</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000837</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000203</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001183</id>
<name>morpholino</name>
<def>
<defstr>An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.</comment>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Morpholino</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000348</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001184</id>
<name>PNA</name>
<def>
<defstr>An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.</comment>
<synonym scope="related">
<synonym_text>peptide nucleic acid</synonym_text>
</synonym>
<is_a>SO:0000348</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001185</id>
<name>enzymatic</name>
<def>
<defstr>An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.</comment>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001186</id>
<name>ribozymic</name>
<def>
<defstr>An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.</comment>
<is_a>SO:0001185</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001187</id>
<name>pseudouridylation_guide_snoRNA</name>
<def>
<defstr>A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.</defstr>
<dbxref>
<acc>mah</acc>
<dbname>GOC</dbname>
</dbxref>
<dbxref>
<acc>12457565</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>Has RNA pseudouridylation guide activity (GO:0030558).</comment>
<synonym scope="exact">
<synonym_text>pseudouridylation guide snoRNA</synonym_text>
</synonym>
<is_a>SO:0000594</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001188</id>
<name>LNA</name>
<def>
<defstr>An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.</defstr>
<dbxref>
<acc>48010</acc>
<dbname>CHEBI</dbname>
</dbxref>
</def>
<comment>Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.</comment>
<is_a>SO:0000348</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001189</id>
<name>LNA_oligo</name>
<def>
<defstr>An oligo composed of LNA residues.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>LNA oligo</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>locked nucleic acid</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Locked_nucleic_acid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001247</is_a>
<intersection_of>
<to>SO:0001247</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001188</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001190</id>
<name>TNA</name>
<def>
<defstr>An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.</defstr>
<dbxref>
<acc>48019</acc>
<dbname>CHEBI</dbname>
</dbxref>
</def>
<comment>Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.</comment>
<is_a>SO:0000348</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001191</id>
<name>TNA_oligo</name>
<def>
<defstr>An oligo composed of TNA residues.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>threose nucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>TNA oligo</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Threose_nucleic_acid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001247</is_a>
<intersection_of>
<to>SO:0001247</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001190</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001192</id>
<name>GNA</name>
<def>
<defstr>An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.</defstr>
<dbxref>
<acc>48015</acc>
<dbname>CHEBI</dbname>
</dbxref>
</def>
<comment>Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.</comment>
<is_a>SO:0000348</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001193</id>
<name>GNA_oligo</name>
<def>
<defstr>An oligo composed of GNA residues.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>glycerol nucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>glycol nucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>GNA oligo</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Glycerol_nucleic_acid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001247</is_a>
<intersection_of>
<to>SO:0001247</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001192</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001194</id>
<name>R_GNA</name>
<def>
<defstr>An attribute describing a GNA sequence in the (R)-GNA enantiomer.</defstr>
<dbxref>
<acc>48016</acc>
<dbname>CHEBI</dbname>
</dbxref>
</def>
<comment>Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.</comment>
<synonym scope="exact">
<synonym_text>R GNA</synonym_text>
</synonym>
<is_a>SO:0001192</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001195</id>
<name>R_GNA_oligo</name>
<def>
<defstr>An oligo composed of (R)-GNA residues.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>(R)-glycerol nucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>(R)-glycol nucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>R GNA oligo</synonym_text>
</synonym>
<is_a>SO:0001193</is_a>
<intersection_of>
<to>SO:0001193</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001194</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001196</id>
<name>S_GNA</name>
<def>
<defstr>An attribute describing a GNA sequence in the (S)-GNA enantiomer.</defstr>
<dbxref>
<acc>48017</acc>
<dbname>CHEBI</dbname>
</dbxref>
</def>
<comment>Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.</comment>
<synonym scope="exact">
<synonym_text>S GNA</synonym_text>
</synonym>
<is_a>SO:0001192</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001197</id>
<name>S_GNA_oligo</name>
<def>
<defstr>An oligo composed of (S)-GNA residues.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>(S)-glycerol nucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>(S)-glycol nucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>S GNA oligo</synonym_text>
</synonym>
<is_a>SO:0001193</is_a>
<intersection_of>
<to>SO:0001193</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001196</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001198</id>
<name>ds_DNA_viral_sequence</name>
<def>
<defstr>A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>double stranded DNA virus</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ds DNA viral sequence</synonym_text>
</synonym>
<is_a>SO:0001041</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001199</id>
<name>ss_RNA_viral_sequence</name>
<def>
<defstr>A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>single strand RNA virus</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ss RNA viral sequence</synonym_text>
</synonym>
<is_a>SO:0001041</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001200</id>
<name>negative_sense_ssRNA_viral_sequence</name>
<def>
<defstr>A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>negative sense single stranded RNA virus</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>negative sense ssRNA viral sequence</synonym_text>
</synonym>
<is_a>SO:0001199</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001201</id>
<name>positive_sense_ssRNA_viral_sequence</name>
<def>
<defstr>A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>positive sense single stranded RNA virus</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>positive sense ssRNA viral sequence</synonym_text>
</synonym>
<is_a>SO:0001199</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001202</id>
<name>ambisense_ssRNA_viral_sequence</name>
<def>
<defstr>A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>ambisense single stranded RNA virus</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ambisense ssRNA viral sequence</synonym_text>
</synonym>
<is_a>SO:0001199</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001203</id>
<name>RNA_polymerase_promoter</name>
<def>
<defstr>A region (DNA) to which RNA polymerase binds, to begin transcription.</defstr>
<dbxref>
<acc>jb</acc>
<dbname>xenbase</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>RNA polymerase promoter</synonym_text>
</synonym>
<is_a>SO:0000167</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001204</id>
<name>Phage_RNA_Polymerase_Promoter</name>
<def>
<defstr>A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.</defstr>
<dbxref>
<acc>jb</acc>
<dbname>xenbase</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>Phage RNA Polymerase Promoter</synonym_text>
</synonym>
<is_a>SO:0001203</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001205</id>
<name>SP6_RNA_Polymerase_Promoter</name>
<def>
<defstr>A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.</defstr>
<dbxref>
<acc>jb</acc>
<dbname>xenbase</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>SP6 RNA Polymerase Promoter</synonym_text>
</synonym>
<is_a>SO:0001204</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001206</id>
<name>T3_RNA_Polymerase_Promoter</name>
<def>
<defstr>A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.</defstr>
<dbxref>
<acc>jb</acc>
<dbname>xenbase</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>T3 RNA Polymerase Promoter</synonym_text>
</synonym>
<is_a>SO:0001204</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001207</id>
<name>T7_RNA_Polymerase_Promoter</name>
<def>
<defstr>A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.</defstr>
<dbxref>
<acc>jb</acc>
<dbname>xenbase</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>T7 RNA Polymerase Promoter</synonym_text>
</synonym>
<is_a>SO:0001204</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001208</id>
<name>five_prime_EST</name>
<def>
<defstr>An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov/About/primer/est.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5' EST</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime EST</synonym_text>
</synonym>
<is_a>SO:0000345</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001209</id>
<name>three_prime_EST</name>
<def>
<defstr>An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov/About/primer/est.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3' EST</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime EST</synonym_text>
</synonym>
<is_a>SO:0000345</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001210</id>
<name>translational_frameshift</name>
<def>
<defstr>The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>ribosomal frameshift</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>translational frameshift</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Translational_frameshift</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000836</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001211</id>
<name>plus_1_translational_frameshift</name>
<def>
<defstr>The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>plus 1 ribosomal frameshift</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>plus 1 translational frameshift</synonym_text>
</synonym>
<is_a>SO:0001210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001212</id>
<name>plus_2_translational_frameshift</name>
<def>
<defstr>The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>plus 2 ribosomal frameshift</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>plus 2 translational frameshift</synonym_text>
</synonym>
<is_a>SO:0001210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001213</id>
<name>group_III_intron</name>
<def>
<defstr>Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.</defstr>
<dbxref>
<acc>11377794</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>GO:0000374.</comment>
<synonym scope="exact">
<synonym_text>group III intron</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Group_III_intron</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000588</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001214</id>
<name>noncoding_region_of_exon</name>
<def>
<defstr>The maximal intersection of exon and UTR.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>An exon either containing but not starting with a start codon or containing but not ending with astop codon will be partially coding and partially non coding.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>noncoding region of exon</synonym_text>
</synonym>
<is_a>SO:0000852</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001215</id>
<name>coding_region_of_exon</name>
<def>
<defstr>The region of an exon that encodes for protein sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>An exon containing either a start or stop codon will be partially coding and partially non coding.</comment>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>coding region of exon</synonym_text>
</synonym>
<is_a>SO:0000852</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001216</id>
<name>endonuclease_spliced_intron</name>
<def>
<defstr>An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>endonuclease spliced intron</synonym_text>
</synonym>
<is_a>SO:0000188</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001217</id>
<name>protein_coding_gene</name>
<synonym scope="exact">
<synonym_text>protein coding gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000010</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001218</id>
<name>transgenic_insertion</name>
<def>
<defstr>An insertion that derives from another organism, via the use of recombinant DNA technology.</defstr>
<dbxref>
<acc>bm</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>transgenic insertion</synonym_text>
</synonym>
<is_a>SO:0000667</is_a>
<intersection_of>
<to>SO:0000667</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000781</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001219</id>
<name>retrogene</name>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000569</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001220</id>
<name>silenced_by_RNA_interference</name>
<def>
<defstr>An attribute describing an epigenetic process where a gene is inactivated by RNA interference.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>RNA interference is GO:0016246.</comment>
<synonym scope="exact">
<synonym_text>silenced by RNA interference</synonym_text>
</synonym>
<is_a>SO:0000893</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001221</id>
<name>silenced_by_histone_modification</name>
<def>
<defstr>An attribute describing an epigenetic process where a gene is inactivated by histone modification.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>Histone modification is GO:0016570.</comment>
<synonym scope="exact">
<synonym_text>silenced by histone modification</synonym_text>
</synonym>
<is_a>SO:0000893</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001222</id>
<name>silenced_by_histone_methylation</name>
<def>
<defstr>An attribute describing an epigenetic process where a gene is inactivated by histone methylation.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>Histone methylation is GO:0016571.</comment>
<synonym scope="exact">
<synonym_text>silenced by histone methylation</synonym_text>
</synonym>
<is_a>SO:0001221</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001223</id>
<name>silenced_by_histone_deacetylation</name>
<def>
<defstr>An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>Histone deacetylation is GO:0016573.</comment>
<synonym scope="exact">
<synonym_text>silenced by histone deacetylation</synonym_text>
</synonym>
<is_a>SO:0001221</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001224</id>
<name>gene_silenced_by_RNA_interference</name>
<def>
<defstr>A gene that is silenced by RNA interference.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene silenced by RNA interference</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RNA interference silenced gene</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RNAi silenced gene</synonym_text>
</synonym>
<is_a>SO:0000127</is_a>
<intersection_of>
<to>SO:0000127</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001220</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001225</id>
<name>gene_silenced_by_histone_modification</name>
<def>
<defstr>A gene that is silenced by histone modification.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene silenced by histone modification</synonym_text>
</synonym>
<is_a>SO:0000127</is_a>
<intersection_of>
<to>SO:0000127</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001221</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001226</id>
<name>gene_silenced_by_histone_methylation</name>
<def>
<defstr>A gene that is silenced by histone methylation.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene silenced by histone methylation</synonym_text>
</synonym>
<is_a>SO:0001225</is_a>
<intersection_of>
<to>SO:0001225</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001222</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001227</id>
<name>gene_silenced_by_histone_deacetylation</name>
<def>
<defstr>A gene that is silenced by histone deacetylation.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene silenced by histone deacetylation</synonym_text>
</synonym>
<is_a>SO:0001225</is_a>
<intersection_of>
<to>SO:0001225</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001223</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001228</id>
<name>dihydrouridine</name>
<def>
<defstr>A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>D</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Dihydrouridine</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<xref_analog>
<acc>051</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001229</id>
<name>pseudouridine</name>
<def>
<defstr>A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>The free molecule is CHEBI:17802.</comment>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>Y</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Pseudouridine</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<xref_analog>
<acc>050</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001230</id>
<name>inosine</name>
<def>
<defstr>A modified RNA base in which hypoxanthine is bound to the ribose ring.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>The free molecule is CHEBI:17596.</comment>
<synonym scope="related">
<synonym_text>I</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>RNAMOD:017</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Inosine</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000250</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001231</id>
<name>seven_methylguanine</name>
<def>
<defstr>A modified RNA base in which guanine is methylated at the 7- position.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>The free molecule is CHEBI:2274.</comment>
<synonym scope="exact">
<synonym_text>7-methylguanine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>seven methylguanine</synonym_text>
</synonym>
<is_a>SO:0000250</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001232</id>
<name>ribothymidine</name>
<def>
<defstr>A modified RNA base in which thymine is bound to the ribose ring.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>The free molecule is CHEBI:30832.</comment>
<is_a>SO:0000250</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001233</id>
<name>methylinosine</name>
<def>
<defstr>A modified RNA base in which methylhypoxanthine is bound to the ribose ring.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<is_a>SO:0001274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001234</id>
<name>mobile</name>
<def>
<defstr>An attribute describing a feature that has either intra-genome or intracellular mobility.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Mobile</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000733</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001235</id>
<name>replicon</name>
<def>
<defstr>A region containing at least one unique origin of replication and a unique termination site.</defstr>
<dbxref>
<acc>0716719207</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Replicon_(genetics)</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001236</id>
<name>base</name>
<def>
<defstr>A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Nucleobase</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000001</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001237</id>
<name>amino_acid</name>
<def>
<defstr>A sequence feature that corresponds to a single amino acid residue in a polypeptide.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<comment>Probably in the future this will cross reference to Chebi.</comment>
<synonym scope="exact">
<synonym_text>amino acid</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Amino_acid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001411</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000104</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001238</id>
<name>major_TSS</name>
<synonym scope="exact">
<synonym_text>major transcription start site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>major TSS</synonym_text>
</synonym>
<is_a>SO:0000315</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001239</id>
<name>minor_TSS</name>
<synonym scope="exact">
<synonym_text>minor TSS</synonym_text>
</synonym>
<is_a>SO:0000315</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001240</id>
<name>TSS_region</name>
<def>
<defstr>The region of a gene from the 5' most TSS to the 3' TSS.</defstr>
<dbxref>
<acc>nw</acc>
<dbname>BBOP</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>TSS region</synonym_text>
</synonym>
<is_a>SO:0000842</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000315</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001241</id>
<name>encodes_alternate_transcription_start_sites</name>
<synonym scope="exact">
<synonym_text>encodes alternate transcription start sites</synonym_text>
</synonym>
<is_a>SO:0000401</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001243</id>
<name>miRNA_primary_transcript_region</name>
<def>
<defstr>A part of an miRNA primary_transcript.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>miRNA primary transcript region</synonym_text>
</synonym>
<is_a>SO:0000835</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001244</id>
<name>pre_miRNA</name>
<def>
<defstr>The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin sructure.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>pre-miRNA</synonym_text>
</synonym>
<is_a>SO:0001243</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000647</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001245</id>
<name>miRNA_stem</name>
<def>
<defstr>The stem of the hairpin loop formed by folding of the pre-miRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>miRNA stem</synonym_text>
</synonym>
<is_a>SO:0001243</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0001244</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001246</id>
<name>miRNA_loop</name>
<def>
<defstr>The loop of the hairpin loop formed by folding of the pre-miRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>miRNA loop</synonym_text>
</synonym>
<is_a>SO:0001243</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0001244</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001247</id>
<name>synthetic_oligo</name>
<def>
<defstr>An oligo composed of synthetic nucleotides.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>synthetic oligo</synonym_text>
</synonym>
<is_a>SO:0000696</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001248</id>
<name>assembly</name>
<def>
<defstr>A region of the genome of known length that is composed by ordering and aligning two or more different regions.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001410</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001249</id>
<name>fragment_assembly</name>
<def>
<defstr>A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>fragment assembly</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>physical map</synonym_text>
</synonym>
<is_a>SO:0001248</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001250</id>
<name>fingerprint_map</name>
<def>
<defstr>A fingerprint_map is a physical map composed of restriction fragments.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>BACmap</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>fingerprint map</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>FPC</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>FPCmap</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>restriction map</synonym_text>
</synonym>
<is_a>SO:0001249</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000412</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001251</id>
<name>STS_map</name>
<def>
<defstr>An STS map is a physical map organized by the unique STS landmarks.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>STS map</synonym_text>
</synonym>
<is_a>SO:0001249</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000331</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001252</id>
<name>RH_map</name>
<def>
<defstr>A radiation hybrid map is a physical map.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>radiation hybrid map</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>RH map</synonym_text>
</synonym>
<is_a>SO:0001249</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000331</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001253</id>
<name>sonicate_fragment</name>
<def>
<defstr>A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>sonicate fragment</synonym_text>
</synonym>
<is_a>SO:0000143</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001254</id>
<name>polyploid</name>
<def>
<defstr>A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Polyploid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:1000182</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001255</id>
<name>autopolyploid</name>
<def>
<defstr>A polyploid where the multiple chromosome set was derived from the same organism.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Autopolyploid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001254</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001256</id>
<name>allopolyploid</name>
<def>
<defstr>A polyploid where the multiple chromosome set was derived from a different organism.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Allopolyploid</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001254</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001257</id>
<name>homing_endonuclease_binding_site</name>
<def>
<defstr>The binding site (recognition site) of a homing endonuclease. The binding site is typically large.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>homing endonuclease binding site</synonym_text>
</synonym>
<is_a>SO:0000059</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001258</id>
<name>octamer_motif</name>
<def>
<defstr>A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.</defstr>
<dbxref>
<acc>dh</acc>
<dbname>GOC</dbname>
</dbxref>
<dbxref>
<acc>3095662</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>Nature. 1986 Oct 16-22;323(6089):640-3.</comment>
<synonym scope="exact">
<synonym_text>octamer motif</synonym_text>
</synonym>
<is_a>SO:0000235</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000170</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001259</id>
<name>apicoplast_chromosome</name>
<def>
<defstr>A chromosome originating in an apicoplast.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>apicoplast chromosome</synonym_text>
</synonym>
<is_a>SO:0000340</is_a>
<intersection_of>
<to>SO:0000340</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000743</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001260</id>
<name>sequence_collection</name>
<def>
<defstr>A collection of discontinuous sequences.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>sequence collection</synonym_text>
</synonym>
<namespace>sequence</namespace>
<is_root>1</is_root>
</term>
<term>
<id>SO:0001261</id>
<name>overlapping_feature_set</name>
<def>
<defstr>A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This feature was requested by nicole, tracker id 1911479. It is required to gather evidense together for annotation. An example would be overlapping ESTs that support an mRNA.</comment>
<synonym scope="exact">
<synonym_text>overlapping feature set</synonym_text>
</synonym>
<is_a>SO:0000703</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001262</id>
<name>overlapping_EST_set</name>
<def>
<defstr>A continous experimental result region extending the length of multiple overlapping EST's.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>overlapping EST set</synonym_text>
</synonym>
<is_a>SO:0001261</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000345</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001263</id>
<name>ncRNA_gene</name>
<synonym scope="exact">
<synonym_text>ncRNA gen</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ncRNA gene</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>non-coding RNA gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001264</id>
<name>gRNA_gene</name>
<synonym scope="exact">
<synonym_text>gRNA gene</synonym_text>
</synonym>
<is_a>SO:0001263</is_a>
<intersection_of>
<to>SO:0001263</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000979</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001265</id>
<name>miRNA_gene</name>
<synonym scope="exact">
<synonym_text>miRNA gene</synonym_text>
</synonym>
<is_a>SO:0001263</is_a>
<intersection_of>
<to>SO:0001263</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000571</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001266</id>
<name>scRNA_gene</name>
<synonym scope="exact">
<synonym_text>scRNA gene</synonym_text>
</synonym>
<is_a>SO:0001263</is_a>
<intersection_of>
<to>SO:0001263</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000575</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001267</id>
<name>snoRNA_gene</name>
<synonym scope="exact">
<synonym_text>snoRNA gene</synonym_text>
</synonym>
<is_a>SO:0001263</is_a>
<intersection_of>
<to>SO:0001263</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000578</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001268</id>
<name>snRNA_gene</name>
<synonym scope="exact">
<synonym_text>snRNA gene</synonym_text>
</synonym>
<is_a>SO:0001263</is_a>
<intersection_of>
<to>SO:0001263</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0001263</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001269</id>
<name>SRP_RNA_gene</name>
<synonym scope="exact">
<synonym_text>SRP RNA gene</synonym_text>
</synonym>
<is_a>SO:0001263</is_a>
<intersection_of>
<to>SO:0001263</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000642</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001270</id>
<name>stRNA_gene</name>
<synonym scope="exact">
<synonym_text>stRNA gene</synonym_text>
</synonym>
<is_a>SO:0001263</is_a>
<intersection_of>
<to>SO:0001263</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000656</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001271</id>
<name>tmRNA_gene</name>
<synonym scope="exact">
<synonym_text>tmRNA gene</synonym_text>
</synonym>
<is_a>SO:0001263</is_a>
<intersection_of>
<to>SO:0001263</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000659</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001272</id>
<name>tRNA_gene</name>
<synonym scope="exact">
<synonym_text>tRNA gene</synonym_text>
</synonym>
<is_a>SO:0001263</is_a>
<intersection_of>
<to>SO:0001263</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000663</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001273</id>
<name>modified_adenosine</name>
<def>
<defstr>A modified adenine is an adenine base feature that has been altered.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified adenosine</synonym_text>
</synonym>
<is_a>SO:0000250</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001274</id>
<name>modified_inosine</name>
<def>
<defstr>A modified inosine is an inosine base feature that has been altered.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified inosine</synonym_text>
</synonym>
<is_a>SO:0001230</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001275</id>
<name>modified_cytidine</name>
<def>
<defstr>A modified cytidine is a cytidine base feature which has been altered.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified cytidine</synonym_text>
</synonym>
<is_a>SO:0000250</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001276</id>
<name>modified_guanosine</name>
<synonym scope="exact">
<synonym_text>modified guanosine</synonym_text>
</synonym>
<is_a>SO:0000250</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001277</id>
<name>modified_uridine</name>
<synonym scope="exact">
<synonym_text>modified uridine</synonym_text>
</synonym>
<is_a>SO:0000250</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001278</id>
<name>one_methylinosine</name>
<def>
<defstr>1-methylinosine is a modified insosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>1-methylinosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m1I</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>one methylinosine</synonym_text>
</synonym>
<xref_analog>
<acc>018</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001279</id>
<name>one_two_prime_O_dimethylinosine</name>
<def>
<defstr>1,2'-O-dimethylinosine is a modified inosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>1,2'-O-dimethylinosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m'Im</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>one two prime O dimethylinosine</synonym_text>
</synonym>
<xref_analog>
<acc>019</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001280</id>
<name>two_prime_O_methylinosine</name>
<def>
<defstr>2'-O-methylinosine is a modified inosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2'-O-methylinosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>Im</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two prime O methylinosine</synonym_text>
</synonym>
<xref_analog>
<acc>081</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001274</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001281</id>
<name>three_methylcytidine</name>
<def>
<defstr>3-methylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3-methylcytidine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m3C</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three methylcytidine</synonym_text>
</synonym>
<xref_analog>
<acc>020</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001282</id>
<name>five_methylcytidine</name>
<def>
<defstr>5-methylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methylcytidine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methylcytidine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m5C</synonym_text>
</synonym>
<xref_analog>
<acc>021</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001283</id>
<name>two_prime_O_methylcytidine</name>
<def>
<defstr>2'-O-methylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2'-O-methylcytidine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>Cm</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two prime O methylcytidine</synonym_text>
</synonym>
<xref_analog>
<acc>022</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001284</id>
<name>two_thiocytidine</name>
<def>
<defstr>2-thiocytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2-thiocytidine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>s2C</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two thiocytidine</synonym_text>
</synonym>
<xref_analog>
<acc>023</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001285</id>
<name>N4_acetylcytidine</name>
<def>
<defstr>N4-acetylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ac4C</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N4 acetylcytidine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N4-acetylcytidine</synonym_text>
</synonym>
<xref_analog>
<acc>024</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001286</id>
<name>five_formylcytidine</name>
<def>
<defstr>5-formylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-formylcytidine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>f5C</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five formylcytidine</synonym_text>
</synonym>
<xref_analog>
<acc>025</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001287</id>
<name>five_two_prime_O_dimethylcytidine</name>
<def>
<defstr>5,2'-O-dimethylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5,2'-O-dimethylcytidine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five two prime O dimethylcytidine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m5Cm</synonym_text>
</synonym>
<xref_analog>
<acc>026</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001288</id>
<name>N4_acetyl_2_prime_O_methylcytidine</name>
<def>
<defstr>N4-acetyl-2'-O-methylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ac4Cm</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N4 acetyl 2 prime O methylcytidine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N4-acetyl-2'-O-methylcytidine</synonym_text>
</synonym>
<xref_analog>
<acc>027</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001289</id>
<name>lysidine</name>
<def>
<defstr>Lysidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>k2C</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Lysidine</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<xref_analog>
<acc>028</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001290</id>
<name>N4_methylcytidine</name>
<def>
<defstr>N4-methylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m4C</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N4 methylcytidine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N4-methylcytidine</synonym_text>
</synonym>
<xref_analog>
<acc>082</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001291</id>
<name>N4_2_prime_O_dimethylcytidine</name>
<def>
<defstr>N4,2'-O-dimethylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m4Cm</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N4 2 prime O dimethylcytidine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N4,2'-O-dimethylcytidine</synonym_text>
</synonym>
<xref_analog>
<acc>083</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001292</id>
<name>five_hydroxymethylcytidine</name>
<def>
<defstr>5-hydroxymethylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-hydroxymethylcytidine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five hydroxymethylcytidine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>hm5C</synonym_text>
</synonym>
<xref_analog>
<acc>084</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001293</id>
<name>five_formyl_two_prime_O_methylcytidine</name>
<def>
<defstr>5-formyl-2'-O-methylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-formyl-2'-O-methylcytidine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>f5Cm</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five formyl two prime O methylcytidine</synonym_text>
</synonym>
<xref_analog>
<acc>095</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001294</id>
<name>N4_N4_2_prime_O_trimethylcytidine</name>
<def>
<defstr>N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m42Cm</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N4,N4,2'-O-trimethylcytidine</synonym_text>
</synonym>
<xref_analog>
<acc>107</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001275</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001295</id>
<name>one_methyladenosine</name>
<def>
<defstr>1_methyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>1-methyladenosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m1A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>one methyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>001</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001296</id>
<name>two_methyladenosine</name>
<def>
<defstr>2_methyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2-methyladenosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m2A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two methyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>002</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001297</id>
<name>N6_methyladenosine</name>
<def>
<defstr>N6_methyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6 methyladenosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6-methyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>003</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001298</id>
<name>two_prime_O_methyladenosine</name>
<def>
<defstr>2prime_O_methyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2'-O-methyladenosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>Am</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two prime O methyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>004</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001299</id>
<name>two_methylthio_N6_methyladenosine</name>
<def>
<defstr>2_methylthio_N6_methyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2-methylthio-N6-methyladenosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ms2m6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two methylthio N6 methyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>005</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001300</id>
<name>N6_isopentenyladenosine</name>
<def>
<defstr>N6_isopentenyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>i6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6 isopentenyladenosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6-isopentenyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>006</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001301</id>
<name>two_methylthio_N6_isopentenyladenosine</name>
<def>
<defstr>2_methylthio_N6_isopentenyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2-methylthio-N6-isopentenyladenosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ms2i6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two methylthio N6 isopentenyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>007</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001302</id>
<name>N6_cis_hydroxyisopentenyl_adenosine</name>
<def>
<defstr>N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>io6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6 cis hydroxyisopentenyl adenosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6-(cis-hydroxyisopentenyl)adenosine</synonym_text>
</synonym>
<xref_analog>
<acc>008</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001303</id>
<name>two_methylthio_N6_cis_hydroxyisopentenyl_adenosine</name>
<def>
<defstr>2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ms2io6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two methylthio N6 cis hydroxyisopentenyl adenosine</synonym_text>
</synonym>
<xref_analog>
<acc>009</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001304</id>
<name>N6_glycinylcarbamoyladenosine</name>
<def>
<defstr>N6_glycinylcarbamoyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>g6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6 glycinylcarbamoyladenosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6-glycinylcarbamoyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>010</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001305</id>
<name>N6_threonylcarbamoyladenosine</name>
<def>
<defstr>N6_threonylcarbamoyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>N6 threonylcarbamoyladenosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6-threonylcarbamoyladenosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>t6A</synonym_text>
</synonym>
<xref_analog>
<acc>011</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001306</id>
<name>two_methylthio_N6_threonyl_carbamoyladenosine</name>
<def>
<defstr>2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2-methylthio-N6-threonyl carbamoyladenosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ms2t6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two methylthio N6 threonyl carbamoyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>012</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001307</id>
<name>N6_methyl_N6_threonylcarbamoyladenosine</name>
<def>
<defstr>N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m6t6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6 methyl N6 threonylcarbamoyladenosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6-methyl-N6-threonylcarbamoyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>013</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001308</id>
<name>N6_hydroxynorvalylcarbamoyladenosine</name>
<def>
<defstr>N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>hn6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6 hydroxynorvalylcarbamoyladenosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6-hydroxynorvalylcarbamoyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>014</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001309</id>
<name>two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine</name>
<def>
<defstr>2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2-methylthio-N6-hydroxynorvalyl carbamoyladenosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ms2hn6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two methylthio N6 hydroxynorvalyl carbamoyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>015</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001310</id>
<name>two_prime_O_ribosyladenosine_phosphate</name>
<def>
<defstr>2prime_O_ribosyladenosine_phosphate is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2'-O-ribosyladenosine (phosphate)</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>Ar(p)</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two prime O ribosyladenosine phosphate</synonym_text>
</synonym>
<xref_analog>
<acc>016</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001311</id>
<name>N6_N6_dimethyladenosine</name>
<def>
<defstr>N6_N6_dimethyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m62A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6,N6-dimethyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>080</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001312</id>
<name>N6_2_prime_O_dimethyladenosine</name>
<def>
<defstr>N6_2prime_O_dimethyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m6Am</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6 2 prime O dimethyladenosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6,2'-O-dimethyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>088</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001313</id>
<name>N6_N6_2_prime_O_trimethyladenosine</name>
<def>
<defstr>N6_N6_2prime_O_trimethyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m62Am</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6,N6,2'-O-trimethyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>089</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001314</id>
<name>one_two_prime_O_dimethyladenosine</name>
<def>
<defstr>1,2'-O-dimethyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>1,2'-O-dimethyladenosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m1Am</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>one two prime O dimethyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>097</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001315</id>
<name>N6_acetyladenosine</name>
<def>
<defstr>N6_acetyladenosine is a modified adenosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ac6A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6 acetyladenosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N6-acetyladenosine</synonym_text>
</synonym>
<xref_analog>
<acc>102</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001273</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001316</id>
<name>seven_deazaguanosine</name>
<def>
<defstr>7-deazaguanosine is a moddified guanosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>7-deazaguanosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>seven deazaguanosine</synonym_text>
</synonym>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001317</id>
<name>queuosine</name>
<def>
<defstr>Queuosine is a modified 7-deazoguanosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>Q</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Queuosine</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<xref_analog>
<acc>043</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001316</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001318</id>
<name>epoxyqueuosine</name>
<def>
<defstr>Epoxyqueuosine is a modified 7-deazoguanosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>eQ</synonym_text>
</synonym>
<xref_analog>
<acc>044</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001316</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001319</id>
<name>galactosyl_queuosine</name>
<def>
<defstr>Galactosyl_queuosine is a modified 7-deazoguanosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>galactosyl queuosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>galactosyl-queuosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>galQ</synonym_text>
</synonym>
<xref_analog>
<acc>045</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001316</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001320</id>
<name>mannosyl_queuosine</name>
<def>
<defstr>Mannosyl_queuosine is a modified 7-deazoguanosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mannosyl queuosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>mannosyl-queuosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>manQ</synonym_text>
</synonym>
<xref_analog>
<acc>046</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001316</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001321</id>
<name>seven_cyano_seven_deazaguanosine</name>
<def>
<defstr>7_cyano_7_deazaguanosine is a modified 7-deazoguanosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>7-cyano-7-deazaguanosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>preQ0</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>seven cyano seven deazaguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>047</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001316</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001322</id>
<name>seven_aminomethyl_seven_deazaguanosine</name>
<def>
<defstr>7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>7-aminomethyl-7-deazaguanosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>preQ1</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>seven aminomethyl seven deazaguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>048</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001316</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001323</id>
<name>archaeosine</name>
<def>
<defstr>Archaeosine is a modified 7-deazoguanosine.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>G+</synonym_text>
</synonym>
<xref_analog>
<acc>049</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001316</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001324</id>
<name>one_methylguanosine</name>
<def>
<defstr>1_methylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>1-methylguanosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m1G</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>one methylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>029</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001325</id>
<name>N2_methylguanosine</name>
<def>
<defstr>N2_methylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m2G</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2 methylguanosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2-methylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>030</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001326</id>
<name>seven_methylguanosine</name>
<def>
<defstr>7_methylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>7-methylguanosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m7G</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>seven methylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>031</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001327</id>
<name>two_prime_O_methylguanosine</name>
<def>
<defstr>2prime_O_methylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2'-O-methylguanosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>Gm</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two prime O methylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>032</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001328</id>
<name>N2_N2_dimethylguanosine</name>
<def>
<defstr>N2_N2_dimethylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m22G</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2,N2-dimethylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>033</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001329</id>
<name>N2_2_prime_O_dimethylguanosine</name>
<def>
<defstr>N2_2prime_O_dimethylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m2Gm</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2 2 prime O dimethylguanosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2,2'-O-dimethylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>034</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001330</id>
<name>N2_N2_2_prime_O_trimethylguanosine</name>
<def>
<defstr>N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m22Gmv</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2,N2,2'-O-trimethylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>035</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001331</id>
<name>two_prime_O_ribosylguanosine_phosphate</name>
<def>
<defstr>2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2'-O-ribosylguanosine (phosphate)</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>Gr(p)</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two prime O ribosylguanosine phosphate</synonym_text>
</synonym>
<xref_analog>
<acc>036</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001332</id>
<name>wybutosine</name>
<def>
<defstr>Wybutosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>yW</synonym_text>
</synonym>
<xref_analog>
<acc>037</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001333</id>
<name>peroxywybutosine</name>
<def>
<defstr>Peroxywybutosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>o2yW</synonym_text>
</synonym>
<xref_analog>
<acc>038</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001334</id>
<name>hydroxywybutosine</name>
<def>
<defstr>Hydroxywybutosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>OHyW</synonym_text>
</synonym>
<xref_analog>
<acc>039</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001335</id>
<name>undermodified_hydroxywybutosine</name>
<def>
<defstr>Undermodified_hydroxywybutosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>OHyW*</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>undermodified hydroxywybutosine</synonym_text>
</synonym>
<xref_analog>
<acc>040</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001336</id>
<name>wyosine</name>
<def>
<defstr>Wyosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>IMG</synonym_text>
</synonym>
<xref_analog>
<acc>041</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001337</id>
<name>methylwyosine</name>
<def>
<defstr>Methylwyosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>mimG</synonym_text>
</synonym>
<xref_analog>
<acc>042</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001338</id>
<name>N2_7_dimethylguanosine</name>
<def>
<defstr>N2_7_dimethylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m2,7G</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2 7 dimethylguanosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2,7-dimethylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>090</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001339</id>
<name>N2_N2_7_trimethylguanosine</name>
<def>
<defstr>N2_N2_7_trimethylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m2,2,7G</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2,N2,7-trimethylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>091</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001340</id>
<name>one_two_prime_O_dimethylguanosine</name>
<def>
<defstr>1_2prime_O_dimethylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>1,2'-O-dimethylguanosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m1Gm</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>one two prime O dimethylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>096</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001341</id>
<name>four_demethylwyosine</name>
<def>
<defstr>4_demethylwyosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>4-demethylwyosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>four demethylwyosine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>imG-14</synonym_text>
</synonym>
<xref_analog>
<acc>100</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001342</id>
<name>isowyosine</name>
<def>
<defstr>Isowyosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>imG2</synonym_text>
</synonym>
<xref_analog>
<acc>101</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001343</id>
<name>N2_7_2prirme_O_trimethylguanosine</name>
<def>
<defstr>N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m2,7Gm</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2 7 2prirme O trimethylguanosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>N2,7,2'-O-trimethylguanosine</synonym_text>
</synonym>
<xref_analog>
<acc>106</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001276</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001344</id>
<name>five_methyluridine</name>
<def>
<defstr>5_methyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methyluridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m5U</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/5-methyluridine</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<xref_analog>
<acc>052</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001345</id>
<name>two_prime_O_methyluridine</name>
<def>
<defstr>2prime_O_methyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2'-O-methyluridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two prime O methyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>Um</synonym_text>
</synonym>
<xref_analog>
<acc>053</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001346</id>
<name>five_two_prime_O_dimethyluridine</name>
<def>
<defstr>5_2_prime_O_dimethyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5,2'-O-dimethyluridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five two prime O dimethyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m5Um</synonym_text>
</synonym>
<xref_analog>
<acc>054</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001347</id>
<name>one_methylpseudouridine</name>
<def>
<defstr>1_methylpseudouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>1-methylpseudouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m1Y</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>one methylpseudouridine</synonym_text>
</synonym>
<xref_analog>
<acc>055</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001348</id>
<name>two_prime_O_methylpseudouridine</name>
<def>
<defstr>2prime_O_methylpseudouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2'-O-methylpseudouridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two prime O methylpseudouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>Ym</synonym_text>
</synonym>
<xref_analog>
<acc>056</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001349</id>
<name>two_thiouridine</name>
<def>
<defstr>2_thiouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2-thiouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>s2U</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two thiouridine</synonym_text>
</synonym>
<xref_analog>
<acc>057</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001350</id>
<name>four_thiouridine</name>
<def>
<defstr>4_thiouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>4-thiouridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>four thiouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>s4U</synonym_text>
</synonym>
<xref_analog>
<acc>058</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001351</id>
<name>five_methyl_2_thiouridine</name>
<def>
<defstr>5_methyl_2_thiouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methyl-2-thiouridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methyl 2 thiouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m5s2U</synonym_text>
</synonym>
<xref_analog>
<acc>059</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001352</id>
<name>two_thio_two_prime_O_methyluridine</name>
<def>
<defstr>2_thio_2prime_O_methyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>2-thio-2'-O-methyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>s2Um</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>two thio two prime O methyluridine</synonym_text>
</synonym>
<xref_analog>
<acc>060</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001353</id>
<name>three_three_amino_three_carboxypropyl_uridine</name>
<def>
<defstr>3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3-(3-amino-3-carboxypropyl)uridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>acp3U</synonym_text>
</synonym>
<xref_analog>
<acc>061</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001354</id>
<name>five_hydroxyuridine</name>
<def>
<defstr>5_hydroxyuridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-hydroxyuridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five hydroxyuridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ho5U</synonym_text>
</synonym>
<xref_analog>
<acc>060</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001355</id>
<name>five_methoxyuridine</name>
<def>
<defstr>5_methoxyuridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methoxyuridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methoxyuridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>mo5U</synonym_text>
</synonym>
<xref_analog>
<acc>063</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001356</id>
<name>uridine_five_oxyacetic_acid</name>
<def>
<defstr>Uridine_5_oxyacetic_acid is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>cmo5U</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>uridine 5-oxyacetic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>uridine five oxyacetic acid</synonym_text>
</synonym>
<xref_analog>
<acc>064</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001357</id>
<name>uridine_five_oxyacetic_acid_methyl_ester</name>
<def>
<defstr>Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>mcmo5U</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>uridine 5-oxyacetic acid methyl ester</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>uridine five oxyacetic acid methyl ester</synonym_text>
</synonym>
<xref_analog>
<acc>065</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001358</id>
<name>five_carboxyhydroxymethyl_uridine</name>
<def>
<defstr>5_carboxyhydroxymethyl_uridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-(carboxyhydroxymethyl)uridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>chm5U</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five carboxyhydroxymethyl uridine</synonym_text>
</synonym>
<xref_analog>
<acc>066</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001359</id>
<name>five_carboxyhydroxymethyl_uridine_methyl_ester</name>
<def>
<defstr>5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-(carboxyhydroxymethyl)uridine methyl ester</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five carboxyhydroxymethyl uridine methyl ester</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>mchm5U</synonym_text>
</synonym>
<xref_analog>
<acc>067</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001360</id>
<name>five_methoxycarbonylmethyluridine</name>
<def>
<defstr>Five_methoxycarbonylmethyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methoxycarbonylmethyluridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methoxycarbonylmethyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>mcm5U</synonym_text>
</synonym>
<xref_analog>
<acc>068</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001361</id>
<name>five_methoxycarbonylmethyl_two_prime_O_methyluridine</name>
<def>
<defstr>Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methoxycarbonylmethyl-2'-O-methyluridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methoxycarbonylmethyl two prime O methyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>mcm5Um</synonym_text>
</synonym>
<xref_analog>
<acc>069</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001362</id>
<name>five_methoxycarbonylmethyl_two_thiouridine</name>
<def>
<defstr>5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methoxycarbonylmethyl-2-thiouridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methoxycarbonylmethyl two thiouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>mcm5s2U</synonym_text>
</synonym>
<xref_analog>
<acc>070</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001363</id>
<name>five_aminomethyl_two_thiouridine</name>
<def>
<defstr>5_aminomethyl_2_thiouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-aminomethyl-2-thiouridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five aminomethyl two thiouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>nm5s2U</synonym_text>
</synonym>
<xref_analog>
<acc>071</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001364</id>
<name>five_methylaminomethyluridine</name>
<def>
<defstr>5_methylaminomethyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methylaminomethyluridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methylaminomethyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>mnm5U</synonym_text>
</synonym>
<xref_analog>
<acc>072</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001365</id>
<name>five_methylaminomethyl_two_thiouridine</name>
<def>
<defstr>5_methylaminomethyl_2_thiouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methylaminomethyl-2-thiouridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methylaminomethyl two thiouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>mnm5s2U</synonym_text>
</synonym>
<xref_analog>
<acc>073</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001366</id>
<name>five_methylaminomethyl_two_selenouridine</name>
<def>
<defstr>5_methylaminomethyl_2_selenouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methylaminomethyl-2-selenouridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methylaminomethyl two selenouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>mnm5se2U</synonym_text>
</synonym>
<xref_analog>
<acc>074</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001367</id>
<name>five_carbamoylmethyluridine</name>
<def>
<defstr>5_carbamoylmethyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-carbamoylmethyluridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five carbamoylmethyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ncm5U</synonym_text>
</synonym>
<xref_analog>
<acc>075</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001368</id>
<name>five_carbamoylmethyl_two_prime_O_methyluridine</name>
<def>
<defstr>5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-carbamoylmethyl-2'-O-methyluridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five carbamoylmethyl two prime O methyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>ncm5Um</synonym_text>
</synonym>
<xref_analog>
<acc>076</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001369</id>
<name>five_carboxymethylaminomethyluridine</name>
<def>
<defstr>5_carboxymethylaminomethyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-carboxymethylaminomethyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>cmnm5U</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five carboxymethylaminomethyluridine</synonym_text>
</synonym>
<xref_analog>
<acc>077</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001370</id>
<name>five_carboxymethylaminomethyl_two_prime_O_methyluridine</name>
<def>
<defstr>5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-carboxymethylaminomethyl- 2'-O-methyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>cmnm5Um</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five carboxymethylaminomethyl two prime O methyluridine</synonym_text>
</synonym>
<xref_analog>
<acc>078</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001371</id>
<name>five_carboxymethylaminomethyl_two_thiouridine</name>
<def>
<defstr>5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-carboxymethylaminomethyl-2-thiouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>cmnm5s2U</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five carboxymethylaminomethyl two thiouridine</synonym_text>
</synonym>
<xref_analog>
<acc>079</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001372</id>
<name>three_methyluridine</name>
<def>
<defstr>3_methyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3-methyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m3U</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three methyluridine</synonym_text>
</synonym>
<xref_analog>
<acc>085</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001373</id>
<name>one_methyl_three_three_amino_three_carboxypropyl_pseudouridine</name>
<def>
<defstr>1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m1acp3Y</synonym_text>
</synonym>
<xref_analog>
<acc>086</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001374</id>
<name>five_carboxymethyluridine</name>
<def>
<defstr>5_carboxymethyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-carboxymethyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>cm5U</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five carboxymethyluridine</synonym_text>
</synonym>
<xref_analog>
<acc>087</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001375</id>
<name>three_two_prime_O_dimethyluridine</name>
<def>
<defstr>3_2prime_O_dimethyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3,2'-O-dimethyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m3Um</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three two prime O dimethyluridine</synonym_text>
</synonym>
<xref_analog>
<acc>092</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001376</id>
<name>five_methyldihydrouridine</name>
<def>
<defstr>5_methyldihydrouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-methyldihydrouridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five methyldihydrouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m5D</synonym_text>
</synonym>
<xref_analog>
<acc>093</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001377</id>
<name>three_methylpseudouridine</name>
<def>
<defstr>3_methylpseudouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3-methylpseudouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>m3Y</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three methylpseudouridine</synonym_text>
</synonym>
<xref_analog>
<acc>094</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001378</id>
<name>five_taurinomethyluridine</name>
<def>
<defstr>5_taurinomethyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-taurinomethyluridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five taurinomethyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>tm5U</synonym_text>
</synonym>
<xref_analog>
<acc>098</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001379</id>
<name>five_taurinomethyl_two_thiouridine</name>
<def>
<defstr>5_taurinomethyl_2_thiouridineis a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-taurinomethyl-2-thiouridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five taurinomethyl two thiouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>tm5s2U</synonym_text>
</synonym>
<xref_analog>
<acc>099</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001380</id>
<name>five_isopentenylaminomethyl_uridine</name>
<def>
<defstr>5_isopentenylaminomethyl_uridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-(isopentenylaminomethyl)uridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five isopentenylaminomethyl uridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>inm5U</synonym_text>
</synonym>
<xref_analog>
<acc>103</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001381</id>
<name>five_isopentenylaminomethyl_two_thiouridine</name>
<def>
<defstr>5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-(isopentenylaminomethyl)- 2-thiouridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five isopentenylaminomethyl two thiouridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>inm5s2U</synonym_text>
</synonym>
<xref_analog>
<acc>104</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001382</id>
<name>five_isopentenylaminomethyl_two_prime_O_methyluridine</name>
<def>
<defstr>5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature.</defstr>
<dbxref>
<acc>http://library.med.utah.edu/RNAmods/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>5-(isopentenylaminomethyl)- 2'-O-methyluridine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five isopentenylaminomethyl two prime O methyluridine</synonym_text>
</synonym>
<synonym synonym_type="RNAMOD" scope="exact">
<synonym_text>inm5Um</synonym_text>
</synonym>
<xref_analog>
<acc>105</acc>
<dbname>RNAMOD</dbname>
</xref_analog>
<is_a>SO:0001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001383</id>
<name>histone_binding_site</name>
<def>
<defstr>A region of a DNA molecule that is bound by a histone.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>histone binding site</synonym_text>
</synonym>
<is_a>SO:0000410</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001384</id>
<name>CDS_fragment</name>
<synonym scope="exact">
<synonym_text>CDS fragment</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>incomplete CDS</synonym_text>
</synonym>
<is_a>SO:0000316</is_a>
<intersection_of>
<to>SO:0000316</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000731</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001385</id>
<name>modified_amino_acid_feature</name>
<def>
<defstr>A post translationally modified amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified amino acid feature</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001386</id>
<name>modified_glycine</name>
<def>
<defstr>A post translationally modified glycine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModGly</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified glycine</synonym_text>
</synonym>
<xref_analog>
<acc>00908</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001387</id>
<name>modified_L_alanine</name>
<def>
<defstr>A post translationally modified alanine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModAla</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L alanine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-alanine</synonym_text>
</synonym>
<xref_analog>
<acc>00901</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001388</id>
<name>modified_L_asparagine</name>
<def>
<defstr>A post translationally modified asparagine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModAsn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L asparagine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-asparagine</synonym_text>
</synonym>
<xref_analog>
<acc>00903</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001389</id>
<name>modified_L_aspartic_acid</name>
<def>
<defstr>A post translationally modified aspartic acid amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModAsp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L aspartic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-aspartic acid</synonym_text>
</synonym>
<xref_analog>
<acc>00904</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001390</id>
<name>modified_L_cysteine</name>
<def>
<defstr>A post translationally modified cysteine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModCys</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L cysteine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-cysteine</synonym_text>
</synonym>
<xref_analog>
<acc>00905</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001391</id>
<name>modified_L_glutamic_acid</name>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModGlu</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L glutamic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-glutamic acid</synonym_text>
</synonym>
<xref_analog>
<acc>00906</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001392</id>
<name>modified_L_threonine</name>
<def>
<defstr>A post translationally modified threonine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L threonine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-threonine</synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModThr</synonym_text>
</synonym>
<xref_analog>
<acc>00917</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001393</id>
<name>modified_L_tryptophan</name>
<def>
<defstr>A post translationally modified tryptophan amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L tryptophan</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-tryptophan</synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModTrp</synonym_text>
</synonym>
<xref_analog>
<acc>00918</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001394</id>
<name>modified_L_glutamine</name>
<def>
<defstr>A post translationally modified glutamine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>ModGln</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L glutamine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-glutamine</synonym_text>
</synonym>
<xref_analog>
<acc>00907</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001395</id>
<name>modified_L_methionine</name>
<def>
<defstr>A post translationally modified methionine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L methionine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-methionine</synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModMet</synonym_text>
</synonym>
<xref_analog>
<acc>00913</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001396</id>
<name>modified_L_isoleucine</name>
<def>
<defstr>A post translationally modified isoleucine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L isoleucine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-isoleucine</synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModIle</synonym_text>
</synonym>
<xref_analog>
<acc>00910</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001397</id>
<name>modified_L_phenylalanine</name>
<def>
<defstr>A post translationally modified phenylalanine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L phenylalanine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-phenylalanine</synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModPhe</synonym_text>
</synonym>
<xref_analog>
<acc>00914</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001398</id>
<name>modified_L_histidine</name>
<def>
<defstr>A post translationally modified histidie amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>ModHis</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L histidine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-histidine</synonym_text>
</synonym>
<xref_analog>
<acc>00909</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001399</id>
<name>modified_L_serine</name>
<def>
<defstr>A post translationally modified serine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L serine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-serine</synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>MosSer</synonym_text>
</synonym>
<xref_analog>
<acc>00916</acc>
<dbname>MOD</dbname>
<name>http://www.psidev.info/index.php?q=node/104</name>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001400</id>
<name>modified_L_lysine</name>
<def>
<defstr>A post translationally modified lysine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L lysine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-lysine</synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModLys</synonym_text>
</synonym>
<xref_analog>
<acc>00912</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001401</id>
<name>modified_L_leucine</name>
<def>
<defstr>A post translationally modified leucine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L leucine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-leucine </synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModLeu</synonym_text>
</synonym>
<xref_analog>
<acc>00911</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001402</id>
<name>modified_L_selenocysteine</name>
<def>
<defstr>A post translationally modified selenocysteine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L selenocysteine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-selenocysteine</synonym_text>
</synonym>
<xref_analog>
<acc>01158</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001403</id>
<name>modified_L_valine</name>
<def>
<defstr>A post translationally modified valine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L valine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-valine</synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModVal</synonym_text>
</synonym>
<xref_analog>
<acc>00920</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001404</id>
<name>modified_L_proline</name>
<def>
<defstr>A post translationally modified proline amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L proline</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-proline </synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModPro</synonym_text>
</synonym>
<xref_analog>
<acc>00915</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001405</id>
<name>modified_L_tyrosine</name>
<def>
<defstr>A post translationally modified tyrosine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>modified L tyrosine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-tyrosine</synonym_text>
</synonym>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModTry</synonym_text>
</synonym>
<xref_analog>
<acc>00919</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001406</id>
<name>modified_L_arginine</name>
<def>
<defstr>A post translationally modified arginine amino acid feature.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym synonym_type="AAMOD" scope="exact">
<synonym_text>ModArg</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L arginine</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>modified L-arginine</synonym_text>
</synonym>
<xref_analog>
<acc>00902</acc>
<dbname>MOD</dbname>
</xref_analog>
<is_a>SO:0001385</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001407</id>
<name>peptidyl</name>
<def>
<defstr>An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000443</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001408</id>
<name>cleaved_for_gpi_anchor_region</name>
<def>
<defstr>The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor.</defstr>
<dbxref>
<acc>rh</acc>
<dbname>EBI</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cleaved for gpi anchor region</synonym_text>
</synonym>
<is_a>SO:0100011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001409</id>
<name>biomaterial_region</name>
<def>
<defstr>A region which is intended for use in an experiment.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>biomaterial region</synonym_text>
</synonym>
<is_a>SO:0000001</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001410</id>
<name>experimental_feature</name>
<def>
<defstr>A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>analysis feature</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>experimental output artefact</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>experimental_output_artefact</synonym_text>
</synonym>
<is_a>SO:0000001</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001411</id>
<name>biological_region</name>
<def>
<defstr>A region defined by its disposition to be involved in a biological process.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>biological region</synonym_text>
</synonym>
<is_a>SO:0000001</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001412</id>
<name>topologically_defined_region</name>
<def>
<defstr>A region that is defined according to its relations with other regions within the same sequence.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>topologically defined region</synonym_text>
</synonym>
<is_a>SO:0000001</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001413</id>
<name>translocation_breakpoint</name>
<def>
<defstr>The point within a chromosome where a translocation begins or ends.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>translocation breakpoint</synonym_text>
</synonym>
<is_a>SO:0001021</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001414</id>
<name>insertion_breakpoint</name>
<def>
<defstr>The point within a chromosome where a insertion begins or ends.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>insertion breakpoint</synonym_text>
</synonym>
<is_a>SO:0001021</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001415</id>
<name>deletion_breakpoint</name>
<def>
<defstr>The point within a chromosome where a deletion begins or ends.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>deletion breakpoint</synonym_text>
</synonym>
<is_a>SO:0001021</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001416</id>
<name>five_prime_flanking_region</name>
<def>
<defstr>A flanking region located five prime of a specific region.</defstr>
<dbxref>
<acc>chado</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>5' flanking region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>five prime flanking region</synonym_text>
</synonym>
<is_a>SO:0000239</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001417</id>
<name>three_prime_flanking_region</name>
<def>
<defstr>A flanking region located three prime of a specific region.</defstr>
<dbxref>
<acc>chado</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>3' flanking region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>three prime flanking region</synonym_text>
</synonym>
<is_a>SO:0000239</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001418</id>
<name>transcribed_fragment</name>
<def>
<defstr>An experimental region, defined by a tiling array experiment to be transcribed at some level.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Term requested by the MODencode group.</comment>
<synonym scope="exact">
<synonym_text>transcribed fragment</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>transfrag</synonym_text>
</synonym>
<is_a>SO:0001410</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001419</id>
<name>cis_splice_site</name>
<def>
<defstr>Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.</defstr>
<dbxref>
<acc>cjm</acc>
<dbname>SO</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>cis splice site</synonym_text>
</synonym>
<is_a>SO:0000162</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001420</id>
<name>trans_splice_site</name>
<def>
<defstr>Primary transcript region bordering trans-splice junction.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>trans splice site</synonym_text>
</synonym>
<is_a>SO:0000162</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001421</id>
<name>splice_junction</name>
<def>
<defstr>The boundary between an intron and an exon.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>splice boundary</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>splice junction</synonym_text>
</synonym>
<is_a>SO:0000699</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001422</id>
<name>conformational_switch</name>
<def>
<defstr>A region of a polypeptide, involved in the transition from one conformational state to another.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999.</comment>
<synonym scope="exact">
<synonym_text>polypeptide conformational switch</synonym_text>
</synonym>
<is_a>SO:0100001</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001423</id>
<name>dye_terminator_read</name>
<def>
<defstr>A read produced by the dye terminator method of sequencing.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>dye terminator read</synonym_text>
</synonym>
<is_a>SO:0000150</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001424</id>
<name>pyrosequenced_read</name>
<def>
<defstr>A read produced by pyrosequencing technology.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>An example is a read produced by Roche 454 technology.</comment>
<synonym scope="related">
<synonym_text>pyorsequenced read</synonym_text>
</synonym>
<is_a>SO:0000150</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001425</id>
<name>ligation_based_read</name>
<def>
<defstr>A read produced by ligation based sequencing technologies.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>An example of this kind of read is one produced by ABI SOLiD.</comment>
<synonym scope="related">
<synonym_text>ligation based read</synonym_text>
</synonym>
<is_a>SO:0000150</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001426</id>
<name>polymerase_synthesis_read</name>
<def>
<defstr>A read produced by the polymerase based sequence by synthesis method.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>An example is a read produced by Illumina technology.</comment>
<synonym scope="related">
<synonym_text>polymerase synthesis read</synonym_text>
</synonym>
<is_a>SO:0000150</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001427</id>
<name>cis_regulatory_frameshift_element</name>
<def>
<defstr>A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence.</defstr>
<dbxref>
<acc>jd</acc>
<dbname>RFAM</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cis regulatory frameshift element</synonym_text>
</synonym>
<is_a>SO:0005836</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001428</id>
<name>expressed_sequence_assembly</name>
<def>
<defstr>A sequence assembly derived from expressed sequences.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>From tracker [ 2372385 ] expressed_sequence_assembly.</comment>
<synonym scope="exact">
<synonym_text>expressed sequence assembly</synonym_text>
</synonym>
<is_a>SO:0000353</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001429</id>
<name>DNA_binding_site</name>
<def>
<defstr>A region of a molecule that binds to DNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>DNA binding site</synonym_text>
</synonym>
<is_a>SO:0000409</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001430</id>
<name>polyA_junction</name>
<def>
<defstr>The boundary between the UTR and the polyA sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>polyA junction</synonym_text>
</synonym>
<is_a>SO:0000699</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001431</id>
<name>cryptic_gene</name>
<def>
<defstr>A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cryptic gene</synonym_text>
</synonym>
<is_a>SO:0000704</is_a>
<intersection_of>
<to>SO:0000704</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000976</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001432</id>
<name>sequence_variant_affecting_polyadenylation</name>
<synonym scope="related">
<synonym_text>mutation affecting polyadenylation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting polyadenylation</synonym_text>
</synonym>
<is_a>SO:1000070</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001433</id>
<name>three_prime_RACE_clone</name>
<def>
<defstr>A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host.</defstr>
<dbxref>
<acc>nlw</acc>
<dbname>modENCODE</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>3' RACE clone</synonym_text>
</synonym>
<is_a>SO:0000317</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001434</id>
<name>cassette_pseudogene</name>
<def>
<defstr>A cassette pseudogene is a kind of gene in an innactive form which may recombine at a telomeric locus to form a functional copy.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Requested by the trypanosome community.</comment>
<synonym scope="exact">
<synonym_text>cassette pseudogene</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>cassette type psedogene</synonym_text>
</synonym>
<is_a>SO:0000336</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001435</id>
<name>alanine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>A</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Ala</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001436</id>
<name>valine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>V</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Val</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001437</id>
<name>leucine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>L</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Leu</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001438</id>
<name>isoleucine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>I</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Ile</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001439</id>
<name>proline</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>P</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Pro</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001440</id>
<name>tryptophan</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Trp</synonym_text>
</synonym>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>W</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001441</id>
<name>phenylalanine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>F</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Phe</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001442</id>
<name>methionine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>M</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Met</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001443</id>
<name>glycine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>G</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Gly</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001444</id>
<name>serine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>S</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Ser</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001445</id>
<name>threonine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>T</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Thr</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001446</id>
<name>tyrosine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Tyr</synonym_text>
</synonym>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>Y</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001447</id>
<name>cysteine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>C</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Cys</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001448</id>
<name>glutamine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Gln</synonym_text>
</synonym>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>Q</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001449</id>
<name>asparagine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Asn</synonym_text>
</synonym>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>N</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001450</id>
<name>lysine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>K</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Lys</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001451</id>
<name>argenine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Arg</synonym_text>
</synonym>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>R</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001452</id>
<name>histidine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>H</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>His</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001453</id>
<name>aspartic_acid</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Asp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>aspartic acid</synonym_text>
</synonym>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>D</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001454</id>
<name>glutamic_acid</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>E</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Glu</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>glutamic acid</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001455</id>
<name>selenocysteine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Sec</synonym_text>
</synonym>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>U</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001456</id>
<name>pyrrolysine</name>
<comment>A place holder for a cross product with chebi.</comment>
<synonym synonym_type="aa1" scope="exact">
<synonym_text>O</synonym_text>
</synonym>
<synonym synonym_type="aa3" scope="exact">
<synonym_text>Pyl</synonym_text>
</synonym>
<is_a>SO:0001237</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001457</id>
<name>transcribed_cluster</name>
<def>
<defstr>A region defined by a set of transcribed sequences from the same gene or expressed pseudogene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term was requested by Jeff Bowes, using the tracker, ID = 2594157.</comment>
<synonym scope="exact">
<synonym_text>transcribed cluster</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>unigene cluster</synonym_text>
</synonym>
<is_a>SO:0001410</is_a>
<relationship>
<type>has_part</type>
<to>SO:0000695</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001458</id>
<name>unigene_cluster</name>
<def>
<defstr>A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term was requested by Jeff Bowes, using the tracker, ID = 2594157.</comment>
<synonym scope="related">
<synonym_text>unigene cluster</synonym_text>
</synonym>
<is_a>SO:0001457</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001459</id>
<name>CRISPR</name>
<def>
<defstr>Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences.</defstr>
<dbxref>
<acc>jd</acc>
<dbname>RFAM</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>Clustered_Regularly_Interspaced_Short_Palindromic_Repeat</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>CRISPR element</synonym_text>
</synonym>
<xref_analog>
<acc>en.wikipedia.org/wiki/CRISPR</acc>
<dbname>http</dbname>
</xref_analog>
<is_a>SO:0000314</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001460</id>
<name>insulator_binding_site</name>
<def>
<defstr>A protein_binding_site located within an insulator.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>See tracker ID 2060908.</comment>
<synonym scope="related">
<synonym_text>insulator binding site</synonym_text>
</synonym>
<is_a>SO:0000410</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000627</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001461</id>
<name>enhancer_binding_site</name>
<def>
<defstr>A protein_binding_site located within an enhancer.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>enhancer binding site</synonym_text>
</synonym>
<is_a>SO:0000410</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000165</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001462</id>
<name>contig_collection</name>
<def>
<defstr>A collection of contigs.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>See tracker ID: 2138359.</comment>
<synonym scope="exact">
<synonym_text>contig collection</synonym_text>
</synonym>
<is_a>SO:0001260</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001463</id>
<name>lincRNA</name>
<def>
<defstr>A multiexonic non-coding RNA transcribed by RNA polymerase II.</defstr>
<dbxref>
<acc>19182780</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>large intervening non-coding RNA</synonym_text>
</synonym>
<is_a>SO:0000655</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001464</id>
<name>UST</name>
<def>
<defstr>An EST spanning part or all of the untranslated regions of a protein-coding transcript.</defstr>
<dbxref>
<acc>nlw</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>UTR sequence tag</synonym_text>
</synonym>
<is_a>SO:0000345</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001465</id>
<name>three_prime_UST</name>
<def>
<defstr>A UST located in the 3'UTR of a protein-coding transcript.</defstr>
<dbxref>
<acc>nlw</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>3' UST</synonym_text>
</synonym>
<is_a>SO:0001464</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001466</id>
<name>five_prime_UST</name>
<def>
<defstr>An UST located in the 5'UTR of a protein-coding transcript.</defstr>
<dbxref>
<acc>nlw</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>5' UST</synonym_text>
</synonym>
<is_a>SO:0001464</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001467</id>
<name>RST</name>
<def>
<defstr>A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long.</defstr>
<dbxref>
<acc>nlw</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>RACE sequence tag</synonym_text>
</synonym>
<is_a>SO:0000345</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001468</id>
<name>three_prime_RST</name>
<def>
<defstr>A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long.</defstr>
<dbxref>
<acc>nlw</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>3' RST</synonym_text>
</synonym>
<is_a>SO:0001467</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001469</id>
<name>five_prime_RST</name>
<def>
<defstr>A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long.</defstr>
<dbxref>
<acc>nlw</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>5' RST</synonym_text>
</synonym>
<is_a>SO:0001467</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001470</id>
<name>UST_match</name>
<def>
<defstr>A match against an UST sequence.</defstr>
<dbxref>
<acc>nlw</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>UST match</synonym_text>
</synonym>
<is_a>SO:0000102</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001471</id>
<name>RST_match</name>
<def>
<defstr>A match against an RST sequence.</defstr>
<dbxref>
<acc>nlw</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>RST match</synonym_text>
</synonym>
<is_a>SO:0000102</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001472</id>
<name>primer_match</name>
<def>
<defstr>A nucleotide match to a primer sequence.</defstr>
<dbxref>
<acc>nlw</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>primer match</synonym_text>
</synonym>
<is_a>SO:0000347</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001473</id>
<name>miRNA_antiguide</name>
<def>
<defstr>A region of the pri miRNA that basepairs with the guide to form the hairpin.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>miRNA antiguide </synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>miRNA passenger strand</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>miRNA star</synonym_text>
</synonym>
<is_a>SO:0001243</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-05-27T03:35:43Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001474</id>
<name>trans_splice_junction</name>
<def>
<defstr>The boundary between the spliced leader and the first exon of the mRNA.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000699</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-07-13T04:50:49Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001475</id>
<name>outron</name>
<def>
<defstr>A region of a primary transcript, that is removed via trans splicing.</defstr>
<dbxref>
<acc>16401417</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000835</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-07-14T11:36:08Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001476</id>
<name>natural_plasmid</name>
<def>
<defstr>A plasmid that occurs naturally.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>natural plasmid</synonym_text>
</synonym>
<is_a>SO:0000155</is_a>
<is_a>SO:0001038</is_a>
<intersection_of>
<type>has_quality</type>
<to>SO:0000782</to>
</intersection_of>
<created_by>kareneilbeck</created_by>
<creation_date>2009-09-01T03:43:06Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001477</id>
<name>gene_trap_construct</name>
<def>
<defstr>A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker.</defstr>
<dbxref>
<acc>dh</acc>
<dbname>ZFIN</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>gene trap construct</synonym_text>
</synonym>
<is_a>SO:0000637</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-09-01T03:49:09Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001478</id>
<name>promoter_trap_construct</name>
<def>
<defstr>A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.</defstr>
<dbxref>
<acc>dh</acc>
<dbname>ZFIN</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>promoter trap construct</synonym_text>
</synonym>
<is_a>SO:0000637</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-09-01T03:52:01Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001479</id>
<name>enhancer_trap_construct</name>
<def>
<defstr>An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic.</defstr>
<dbxref>
<acc>dh</acc>
<dbname>ZFIN</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>enhancer trap construct</synonym_text>
</synonym>
<is_a>SO:0000637</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-09-01T03:53:26Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001480</id>
<name>PAC_end</name>
<def>
<defstr>A region of sequence from the end of a PAC clone that may provide a highly specific marker.</defstr>
<dbxref>
<acc>mh</acc>
<dbname>ZFIN</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>PAC end</synonym_text>
</synonym>
<is_a>SO:0000150</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000154</to>
</relationship>
<created_by>kareneilbeck</created_by>
<creation_date>2009-09-09T05:18:12Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001481</id>
<name>RAPD</name>
<def>
<defstr>RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers.</defstr>
<dbxref>
<acc>mh</acc>
<dbname>ZFIN</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>Random Amplification Polymorphic DNA</synonym_text>
</synonym>
<is_a>SO:0000006</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-09-09T05:26:10Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001482</id>
<name>shadow_enhancer</name>
<is_a>SO:0000165</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-09-09T05:29:29Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001483</id>
<name>SNV</name>
<def>
<defstr>SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist.</defstr>
<dbxref>
<acc>bm</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>single nucleotide variant</synonym_text>
</synonym>
<is_a>SO:1000002</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-10-08T11:37:49Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001484</id>
<name>X_element_combinatorial_repeat</name>
<def>
<defstr>An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element.</defstr>
<dbxref>
<acc>http://www.yeastgenome.org/help/glossary.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>X element combinatorial repeats contain Tbf1p binding sites,nand possible functions include a role in telomerase-independent telomerenmaintenance via recombination or as a barrier against transcriptionalnsilencing. These are usually present as a combination of one or more ofnseveral types of smaller elements (designated A, B, C, or D).</comment>
<synonym scope="exact">
<synonym_text>X element combinatorial repeat</synonym_text>
</synonym>
<is_a>SO:0000657</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000624</to>
</relationship>
<created_by>kareneilbeck</created_by>
<creation_date>2009-11-10T11:03:37Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001485</id>
<name>Y_prime_ element</name>
<def>
<defstr>A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies.</defstr>
<dbxref>
<acc>http://www.yeastgenome.org/help/glossary.html</acc>
<dbname>http</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>Y' element</synonym_text>
</synonym>
<is_a>SO:0000657</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000624</to>
</relationship>
<created_by>kareneilbeck</created_by>
<creation_date>2009-11-10T12:08:57Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001486</id>
<name>standard_draft</name>
<def>
<defstr>The status of a whole genome sequence, where the data is minimally filtered or unfiltered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbor regions of poor quality and can be relatively incomplete.</defstr>
<dbxref>
<acc>10.1126</acc>
<dbname>DOI</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>standard draft</synonym_text>
</synonym>
<is_a>SO:0001499</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-10-23T12:48:32Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001487</id>
<name>high_quality_draft</name>
<def>
<defstr>The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome.</defstr>
<dbxref>
<acc>10.1126</acc>
<dbname>DOI</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>high quality draft</synonym_text>
</synonym>
<is_a>SO:0001499</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-10-23T12:52:36Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001488</id>
<name>improved_high_quality_draft</name>
<def>
<defstr>The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution.</defstr>
<dbxref>
<acc>10.1126</acc>
<dbname>DOI</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>improved high quality draft</synonym_text>
</synonym>
<is_a>SO:0001499</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-10-23T12:54:35Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001489</id>
<name>annotation_directed_improved_draft</name>
<def>
<defstr>The status of a whole genome sequence,where annotation, and verification of coding regions has occurred.</defstr>
<dbxref>
<acc>10.1126</acc>
<dbname>DOI</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>annotation directed improvement</synonym_text>
</synonym>
<is_a>SO:0001499</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-10-23T12:57:10Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001490</id>
<name>noncontiguous_finished</name>
<def>
<defstr>The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions.</defstr>
<dbxref>
<acc>10.1126</acc>
<dbname>DOI</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>non contiguous finished</synonym_text>
</synonym>
<is_a>SO:0001499</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-10-23T01:01:07Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001491</id>
<name>finished_genome</name>
<def>
<defstr>The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.</defstr>
<dbxref>
<acc>10.1126</acc>
<dbname>DOI</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>finished</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>finished genome</synonym_text>
</synonym>
<is_a>SO:0001499</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-10-23T01:04:43Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001492</id>
<name>intronic_regulatory_region</name>
<def>
<defstr>A regulatory region that is part of an intron.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>intronic regulatory region</synonym_text>
</synonym>
<is_a>SO:0005836</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000188</to>
</relationship>
<created_by>kareneilbeck</created_by>
<creation_date>2009-11-08T02:48:02Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001493</id>
<name>centromere_DNA_Element_I</name>
<def>
<defstr>A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus regionncomposed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p).</defstr>
<dbxref>
<acc>11222754</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CDEI</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>Centromere DNA Element I</synonym_text>
</synonym>
<is_a>SO:0000330</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000577</to>
</relationship>
<created_by>kareneilbeck</created_by>
<creation_date>2009-11-09T05:47:23Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001494</id>
<name>centromere_DNA_Element_II</name>
<def>
<defstr>A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.</defstr>
<dbxref>
<acc>11222754</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CDEII</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>centromere DNA Element II</synonym_text>
</synonym>
<is_a>SO:0000330</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000577</to>
</relationship>
<created_by>kareneilbeck</created_by>
<creation_date>2009-11-09T05:51:26Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001495</id>
<name>centromere DNA Element III</name>
<def>
<defstr>A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex.</defstr>
<dbxref>
<acc>11222754</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CDEIII</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>centromere DNA Element III</synonym_text>
</synonym>
<is_a>SO:0000330</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000577</to>
</relationship>
<created_by>kareneilbeck</created_by>
<creation_date>2009-11-09T05:54:47Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001496</id>
<name>telomeric_repeat</name>
<def>
<defstr>The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.</defstr>
<dbxref>
<acc>8720065</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions.</comment>
<synonym scope="exact">
<synonym_text>telomeric repeat</synonym_text>
</synonym>
<is_a>SO:0000657</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000624</to>
</relationship>
<created_by>kareneilbeck</created_by>
<creation_date>2009-11-09T06:00:42Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001497</id>
<name>X_element</name>
<def>
<defstr>The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.</defstr>
<dbxref>
<acc>http://www.yeastgenome.org/help/glossary.html#xelemcoresequence</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Possible functions include roles in chromosomal segregation,nmaintenance of chromosome stability, recombinational sequestering, or as anbarrier to transcriptional silencing.</comment>
<synonym scope="related">
<synonym_text>X element</synonym_text>
</synonym>
<is_a>SO:0000330</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000624</to>
</relationship>
<created_by>kareneilbeck</created_by>
<creation_date>2009-11-10T10:56:54Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001498</id>
<name>YAC_end</name>
<def>
<defstr>A region of sequence from the end of a YAC clone that may provide a highly specific marker.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>YAC end</synonym_text>
</synonym>
<is_a>SO:0000150</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000152</to>
</relationship>
<created_by>kareneilbeck</created_by>
<creation_date>2009-11-19T11:07:18Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0001499</id>
<name>whole_genome_sequence_status</name>
<def>
<defstr>The status of whole genome sequence.</defstr>
<dbxref>
<acc>10.1126</acc>
<dbname>DOI</dbname>
</dbxref>
</def>
<comment>This terms and children were added to SO in resonse to tracker request by patrick chain. The pape:r Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms.</comment>
<synonym scope="exact">
<synonym_text>whole genome sequence status</synonym_text>
</synonym>
<is_a>SO:0000905</is_a>
<created_by>kareneilbeck</created_by>
<creation_date>2009-10-23T12:47:47Z</creation_date>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005836</id>
<name>regulatory_region</name>
<def>
<defstr>A DNA sequence that controls the expression of a gene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>regulatory region</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Regulatory_region</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000831</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005837</id>
<name>U14_snoRNA_primary_transcript</name>
<def>
<defstr>The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.</defstr>
<dbxref>
<acc>2251119</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>4.5S snRNA primary transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>U14 snoRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000232</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005841</id>
<name>methylation_guide_snoRNA</name>
<def>
<defstr>A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.</defstr>
<dbxref>
<acc>mah</acc>
<dbname>GOC</dbname>
</dbxref>
<dbxref>
<acc>12457565</acc>
<dbname>PMID</dbname>
</dbxref>
</def>
<comment>Has RNA 2'-O-ribose methylation guide activity (GO:0030561).</comment>
<synonym scope="exact">
<synonym_text>methylation guide snoRNA</synonym_text>
</synonym>
<is_a>SO:0000593</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000580</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005843</id>
<name>rRNA_cleavage_RNA</name>
<def>
<defstr>An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.</defstr>
<dbxref>
<acc>kgc</acc>
<dbname>GOC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>rRNA cleavage RNA</synonym_text>
</synonym>
<is_a>SO:0000655</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0000582</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005845</id>
<name>exon_of_single_exon_gene</name>
<def>
<defstr>An exon that is the only exon in a gene.</defstr>
<dbxref>
<acc>cb</acc>
<dbname>RSC</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>exon of single exon gene</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>single_exon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>singleton exon</synonym_text>
</synonym>
<is_a>SO:0000147</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005847</id>
<name>cassette_array_member</name>
<synonym scope="exact">
<synonym_text>cassette array member</synonym_text>
</synonym>
<is_a>SO:0005848</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005848</id>
<name>gene_cassette_member</name>
<synonym scope="exact">
<synonym_text>gene cassette member</synonym_text>
</synonym>
<is_a>SO:0000081</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005849</id>
<name>gene_subarray_member</name>
<synonym scope="exact">
<synonym_text>gene subarray member</synonym_text>
</synonym>
<is_a>SO:0000081</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005850</id>
<name>primer_binding_site</name>
<def>
<defstr>Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>primer binding site</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Primer_binding_site</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000409</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000186</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005851</id>
<name>gene_array</name>
<def>
<defstr>An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.</comment>
<synonym scope="exact">
<synonym_text>gene array</synonym_text>
</synonym>
<is_a>SO:0005855</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005852</id>
<name>gene_subarray</name>
<def>
<defstr>A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This would include, for example, a cluster of genes encoding different histones.</comment>
<synonym scope="exact">
<synonym_text>gene subarray</synonym_text>
</synonym>
<is_a>SO:0005855</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005853</id>
<name>gene_cassette</name>
<def>
<defstr>A gene that can be substituted for a related gene at a different site in the genome.</defstr>
<dbxref>
<acc>se</acc>
<dbname>SGD</dbname>
</dbxref>
</def>
<comment>This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid.</comment>
<synonym scope="exact">
<synonym_text>gene cassette</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Gene_cassette</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000704</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005854</id>
<name>gene_cassette_array</name>
<def>
<defstr>An array of non-functional genes whose members, when captured by recombination form functional genes.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This would include, for example, the arrays of non-functional VSG genes of Trypanosomes.</comment>
<synonym scope="exact">
<synonym_text>gene cassette array</synonym_text>
</synonym>
<is_a>SO:0005855</is_a>
<relationship>
<type>has_part</type>
<to>SO:0005853</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005855</id>
<name>gene_group</name>
<def>
<defstr>A collection of related genes.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>gene group</synonym_text>
</synonym>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005856</id>
<name>selenocysteine_tRNA_primary_transcript</name>
<def>
<defstr>A primary transcript encoding seryl tRNA (SO:000269).</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>selenocysteine tRNA primary transcript</synonym_text>
</synonym>
<is_a>SO:0000210</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005857</id>
<name>selenocysteinyl_tRNA</name>
<def>
<defstr>A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>selenocysteinyl tRNA</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>selenocysteinyl-transfer ribonucleic acid</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>selenocysteinyl-transfer RNA</synonym_text>
</synonym>
<is_a>SO:0000253</is_a>
<relationship>
<type>derives_from</type>
<to>SO:0005856</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0005858</id>
<name>syntenic_region</name>
<def>
<defstr>A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.</defstr>
<dbxref>
<acc>http://www.informatics.jax.org/silverbook/glossary.shtml</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>syntenic region</synonym_text>
</synonym>
<is_a>SO:0000330</is_a>
<intersection_of>
<to>SO:0000330</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000860</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100001</id>
<name>biochemical_region_of_peptide</name>
<def>
<defstr>A region of a peptide that is involved in a biochemical function.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>biochemical motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>biochemical region of peptide</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>biochemical_region</synonym_text>
</synonym>
<is_a>SO:0001067</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100002</id>
<name>molecular_contact_region</name>
<def>
<defstr>A region that is involved a contact with another molecule.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>molecular contact region</synonym_text>
</synonym>
<is_a>SO:0100001</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100003</id>
<name>intrinsically_unstructured_polypeptide_region</name>
<def>
<defstr>A region of polypeptide chain with high conformational flexibility.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>disordered region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>intrinsically unstructured polypeptide region</synonym_text>
</synonym>
<is_a>SO:0001070</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100004</id>
<name>catmat_left_handed_three</name>
<def>
<defstr>A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>catmat-3l</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100005</id>
<name>catmat_left_handed_four</name>
<def>
<defstr>A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>catmat-4l</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100006</id>
<name>catmat_right_handed_three</name>
<def>
<defstr>A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>catmat-3r</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100007</id>
<name>catmat_right_handed_four</name>
<def>
<defstr>A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>catmat-4r</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100008</id>
<name>alpha_beta_motif</name>
<def>
<defstr>A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
<dbxref>
<acc>http://www.ebi.ac.uk/msd-srv/msdmotif/</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>alpha beta motif</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100009</id>
<name>lipoprotein_signal_peptide</name>
<def>
<defstr>A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>lipoprotein signal peptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>prokaryotic membrane lipoprotein lipid attachment site</synonym_text>
</synonym>
<is_a>SO:0100011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100010</id>
<name>no_output</name>
<def>
<defstr>An experimental region wherean analysis has been run and not produced any annotation.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="exact">
<synonym_text>no output</synonym_text>
</synonym>
<is_a>SO:0000703</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100011</id>
<name>cleaved_peptide_region</name>
<def>
<defstr>The cleaved_peptide_regon is the a region of peptide sequence that is cleaved during maturation.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>cleaved peptide region</synonym_text>
</synonym>
<is_a>SO:0000839</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0001063</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100012</id>
<name>peptide_coil</name>
<def>
<defstr>Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym synonym_type="BS" scope="related">
<synonym_text>coil</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>peptide coil</synonym_text>
</synonym>
<synonym synonym_type="BS" scope="related">
<synonym_text>random coil</synonym_text>
</synonym>
<is_a>SO:0001078</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100013</id>
<name>hydrophobic_region_of_peptide</name>
<def>
<defstr>Hydrophobic regions are regions with a low affinity for water.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<comment>Range.</comment>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>hydropathic</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>hydrophobic region of peptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>hydrophobic_region</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>hydrophobicity</synonym_text>
</synonym>
<is_a>SO:0000839</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100014</id>
<name>n_terminal_region</name>
<def>
<defstr>The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>N-region</synonym_text>
</synonym>
<is_a>SO:0100011</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000418</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100015</id>
<name>c_terminal_region</name>
<def>
<defstr>The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>C-region</synonym_text>
</synonym>
<is_a>SO:0100011</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000418</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100016</id>
<name>central_hydrophobic_region_of_signal_peptide</name>
<def>
<defstr>The central, hydrophobic region of the signal peptide (approx 7-15 aa).</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>central hydrophobic region of signal peptide</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>central_hydrophobic_region</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>H-region</synonym_text>
</synonym>
<is_a>SO:0100011</is_a>
<relationship>
<type>OBO_REL:part_of</type>
<to>SO:0000418</to>
</relationship>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100017</id>
<name>polypeptide_conserved_motif</name>
<def>
<defstr>A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>motif</synonym_text>
</synonym>
<is_a>SO:0001067</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100018</id>
<name>polypeptide_binding_motif</name>
<def>
<defstr>A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>binding</synonym_text>
<dbxref>
<acc>feature_type</acc>
<dbname>uniprot</dbname>
</dbxref>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide binding motif</synonym_text>
</synonym>
<is_a>SO:0100001</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100019</id>
<name>polypeptide_catalytic_motif</name>
<def>
<defstr>A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="related">
<synonym_text>catalytic_motif</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide catalytic motif</synonym_text>
</synonym>
<is_a>SO:0100001</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100020</id>
<name>polypeptide_DNA_contact</name>
<def>
<defstr>Residues involved in interactions with DNA.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>polypeptide DNA contact</synonym_text>
</synonym>
<is_a>SO:0000409</is_a>
<is_a>SO:0100002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:0100021</id>
<name>polypeptide_conserved_region</name>
<def>
<defstr>A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.</defstr>
<dbxref>
<acc>GAR</acc>
<dbname>EBIBS</dbname>
</dbxref>
</def>
<subset>biosapiens</subset>
<synonym scope="exact">
<synonym_text>polypeptide conserved region</synonym_text>
</synonym>
<is_a>SO:0000839</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000002</id>
<name>substitution</name>
<def>
<defstr>Any change in genomic DNA caused by a single event.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_a>SO:0001059</is_a>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000005</id>
<name>complex_substitution</name>
<def>
<defstr>When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>complex substitution</synonym_text>
</synonym>
<is_a>SO:1000002</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000008</id>
<name>point_mutation</name>
<def>
<defstr>A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.</defstr>
<dbxref>
<acc>immuno_workshop</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="exact">
<synonym_text>point mutation</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Point_mutation</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000009</id>
<name>transition</name>
<def>
<defstr>Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<is_a>SO:0001483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000010</id>
<name>pyrimidine_transition</name>
<def>
<defstr>A substitution of a pyrimidine, C or T, for another pyrimidine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>pyrimidine transition</synonym_text>
</synonym>
<is_a>SO:1000009</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000011</id>
<name>C_to_T_transition</name>
<def>
<defstr>A transition of a cytidine to a thymine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>C to T transition</synonym_text>
</synonym>
<is_a>SO:1000010</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000012</id>
<name>C_to_T_transition_at_pCpG_site</name>
<def>
<defstr>The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>C to T transition at pCpG site</synonym_text>
</synonym>
<is_a>SO:1000011</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000013</id>
<name>T_to_C_transition</name>
<synonym scope="exact">
<synonym_text>T to C transition</synonym_text>
</synonym>
<is_a>SO:1000010</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000014</id>
<name>purine_transition</name>
<def>
<defstr>A substitution of a purine, A or G, for another purine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>purine transition</synonym_text>
</synonym>
<is_a>SO:1000009</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000015</id>
<name>A_to_G_transition</name>
<def>
<defstr>A transition of an adenine to a guanine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>A to G transition</synonym_text>
</synonym>
<is_a>SO:1000014</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000016</id>
<name>G_to_A_transition</name>
<def>
<defstr>A transition of a guanine to an adenine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>G to A transition</synonym_text>
</synonym>
<is_a>SO:1000014</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000017</id>
<name>transversion</name>
<def>
<defstr>Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Transversion</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001483</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000018</id>
<name>pyrimidine_to_purine_transversion</name>
<def>
<defstr>Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>pyrimidine to purine transversion</synonym_text>
</synonym>
<is_a>SO:1000017</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000019</id>
<name>C_to_A_transversion</name>
<def>
<defstr>A transversion from cytidine to adenine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>C to A transversion</synonym_text>
</synonym>
<is_a>SO:1000018</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000020</id>
<name>C_to_G_transversion</name>
<synonym scope="exact">
<synonym_text>C to G transversion</synonym_text>
</synonym>
<is_a>SO:1000018</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000021</id>
<name>T_to_A_transversion</name>
<def>
<defstr>A transversion from T to A.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>T to A transversion</synonym_text>
</synonym>
<is_a>SO:1000018</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000022</id>
<name>T_to_G_transversion</name>
<def>
<defstr>A transversion from T to G.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>T to G transversion</synonym_text>
</synonym>
<is_a>SO:1000018</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000023</id>
<name>purine_to_pyrimidine_transversion</name>
<def>
<defstr>Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>purine to pyrimidine transversion</synonym_text>
</synonym>
<is_a>SO:1000017</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000024</id>
<name>A_to_C_transversion</name>
<def>
<defstr>A transversion from adenine to cytidine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>A to C transversion</synonym_text>
</synonym>
<is_a>SO:1000023</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000025</id>
<name>A_to_T_transversion</name>
<def>
<defstr>A transversion from adenine to thymine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>A to T transversion</synonym_text>
</synonym>
<is_a>SO:1000023</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000026</id>
<name>G_to_C_transversion</name>
<def>
<defstr>A transversion from guanine to cytidine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>G to C transversion</synonym_text>
</synonym>
<is_a>SO:1000023</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000027</id>
<name>G_to_T_transversion</name>
<def>
<defstr>A transversion from guanine to thymine.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>G to T transversion</synonym_text>
</synonym>
<is_a>SO:1000023</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000028</id>
<name>intrachromosomal_mutation</name>
<synonym scope="exact">
<synonym_text>intrachromosomal mutation</synonym_text>
</synonym>
<is_a>SO:1000183</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000029</id>
<name>chromosomal_deletion</name>
<def>
<defstr>An incomplete chromosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(bacteria)&ampDgr;</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>(Drosophila)Df</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>(fungi)D</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>chromosomal deletion</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>deficiency</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Chromosomal_deletion</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000550</is_a>
<is_a>SO:1000028</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000030</id>
<name>chromosomal_inversion</name>
<synonym scope="related">
<synonym_text>(bacteria)IN</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>(Drosophila)In</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>(fungi)In</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>chromosomal inversion</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Chromosomal_inversion</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:1000028</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000031</id>
<name>interchromosomal_mutation</name>
<synonym scope="exact">
<synonym_text>interchromosomal mutation</synonym_text>
</synonym>
<is_a>SO:1000183</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000032</id>
<name>indel</name>
<def>
<defstr>A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
<dbxref>
<acc>http://www.hgvs.org/mutnomen/recs-DNA.html#indel</acc>
<dbname>http</dbname>
</dbxref>
</def>
<comment>Indels can have a different number of bases than the corresponding reference sequence.</comment>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Indel</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0001059</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000035</id>
<name>duplication</name>
<def>
<defstr>One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>nucleotide duplication</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>nucleotide_duplication</synonym_text>
</synonym>
<is_a>SO:0000667</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000036</id>
<name>inversion</name>
<def>
<defstr>A continuous nucleotide sequence is inverted in the same position.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_a>SO:0001059</is_a>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000037</id>
<name>chromosomal_duplication</name>
<def>
<defstr>An extra chromosome.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)Dp</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>(fungi)Dp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>chromosomal duplication</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Chromosomal_duplication</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0000550</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000038</id>
<name>intrachromosomal_duplication</name>
<synonym scope="exact">
<synonym_text>intrachromosomal duplication</synonym_text>
</synonym>
<is_a>SO:1000028</is_a>
<is_a>SO:1000037</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000039</id>
<name>direct_tandem_duplication</name>
<synonym scope="exact">
<synonym_text>direct tandem duplication</synonym_text>
</synonym>
<is_a>SO:1000173</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000040</id>
<name>inverted_tandem_duplication</name>
<synonym scope="exact">
<synonym_text>inverted tandem duplication</synonym_text>
</synonym>
<is_a>SO:1000173</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000041</id>
<name>intrachromosomal_transposition</name>
<synonym scope="related">
<synonym_text>(Drosophila)Tp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>intrachromosomal transposition</synonym_text>
</synonym>
<is_a>SO:0000453</is_a>
<is_a>SO:1000038</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000042</id>
<name>compound_chromosome</name>
<synonym scope="exact">
<synonym_text>compound chromosome</synonym_text>
</synonym>
<is_a>SO:1000183</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000043</id>
<name>Robertsonian_fusion</name>
<synonym scope="exact">
<synonym_text>Robertsonian fusion</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Robertsonian_fusion</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:1000044</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000044</id>
<name>chromosomal_translocation</name>
<synonym scope="related">
<synonym_text>(Drosophila)T</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>(fungi)T</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>chromosomal translocation</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Chromosomal_translocation</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:1000031</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000045</id>
<name>ring_chromosome</name>
<synonym scope="related">
<synonym_text>(Drosophila)R</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>(fungi)C</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>ring chromosome</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Ring_chromosome</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:1000028</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000046</id>
<name>pericentric_inversion</name>
<synonym scope="exact">
<synonym_text>pericentric inversion</synonym_text>
</synonym>
<is_a>SO:1000030</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000047</id>
<name>paracentric_inversion</name>
<synonym scope="exact">
<synonym_text>paracentric inversion</synonym_text>
</synonym>
<is_a>SO:1000030</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000048</id>
<name>reciprocal_chromosomal_translocation</name>
<synonym scope="exact">
<synonym_text>reciprocal chromosomal translocation</synonym_text>
</synonym>
<is_a>SO:1000044</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000049</id>
<name>sequence_variation_affecting_transcript</name>
<def>
<defstr>Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mutation affecting transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variation affecting transcript</synonym_text>
</synonym>
<is_a>SO:1000132</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000050</id>
<name>sequence_variant_causing_no_change_in_transcript</name>
<def>
<defstr>No effect on the state of the RNA.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing no change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing no change in transcript</synonym_text>
</synonym>
<is_a>SO:1000049</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000052</id>
<name>sequence_variation_affecting_complex_change_in_transcript</name>
<synonym scope="exact">
<synonym_text>mutation affecting complex change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variation affecting complex change in transcript</synonym_text>
</synonym>
<is_a>SO:1000049</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000054</id>
<name>sequence_variation_affecting_coding_sequence</name>
<def>
<defstr>Any of the amino acid coding triplets of a gene are affected by the DNA mutation.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mutation affecting coding sequence</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>sequence variation affecting coding sequence</synonym_text>
</synonym>
<is_a>SO:1000079</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000055</id>
<name>sequence_variant_causing_initiator_codon_change_in_transcript</name>
<def>
<defstr>The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing initiator codon change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing initiator codon change in transcript</synonym_text>
</synonym>
<is_a>SO:1000056</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000056</id>
<name>sequence_variant_causing_amino_acid_coding_codon_change_in_transcript</name>
<def>
<defstr>The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutaton causing amino acid coding codon change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing amino acid coding codon change in transcript</synonym_text>
</synonym>
<is_a>SO:1000054</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000057</id>
<name>sequence_variant_causing_synonymous_codon_change_in_transcript</name>
<def>
<defstr>The changed codon has the same translation product as the original codon.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing synonymous codon change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing synonymous codon change in transcript</synonym_text>
</synonym>
<is_a>SO:1000056</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000058</id>
<name>sequence_variant_causing_non_synonymous_codon_change_in_transcript</name>
<def>
<defstr>A DNA point mutation that causes a substitution of an amino acid by an other.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing non synonymous codon change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>non-synonymous codon change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing non synonymous codon change in transcript</synonym_text>
</synonym>
<is_a>SO:1000056</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000059</id>
<name>sequence_variant_causing_missense_codon_change_in_transcript</name>
<def>
<defstr>The nucleotide change in the codon leads to a new codon coding for a new amino acid.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing missense codon change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing missense codon change in transcript</synonym_text>
</synonym>
<is_a>SO:1000058</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000060</id>
<name>sequence_variant_causing_conservative_missense_codon_change_in_transcript</name>
<def>
<defstr>The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.</comment>
<synonym scope="related">
<synonym_text>mutation causing conservative missense codon change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing conservative missense codon change in transcript</synonym_text>
</synonym>
<is_a>SO:1000059</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000061</id>
<name>sequence_variant_causing_nonconservative_missense_codon_change_in_transcript</name>
<def>
<defstr>The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.</comment>
<synonym scope="related">
<synonym_text>mutation causing nonconservative missense codon change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing nonconservative missense codon change in transcript</synonym_text>
</synonym>
<is_a>SO:1000059</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000062</id>
<name>sequence_variant_causing_nonsense_codon_change_in_transcript</name>
<def>
<defstr>The nucleotide change in the codon triplet creates a terminator codon.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing nonsense codon change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing nonsense codon change in transcript</synonym_text>
</synonym>
<is_a>SO:1000056</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000063</id>
<name>sequence_variant_causing_terminator_codon_change_in_transcript</name>
<def>
<defstr>The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing terminator codon change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing terminator codon change in transcript</synonym_text>
</synonym>
<is_a>SO:1000054</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000064</id>
<name>sequence_variation_affecting_reading_frame</name>
<def>
<defstr>An umbrella term for terms describing an effect of a sequence variation on the frame of translation.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mutation affecting reading frame</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>sequence variation affecting reading frame</synonym_text>
</synonym>
<is_a>SO:1000054</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000065</id>
<name>frameshift_sequence_variation</name>
<def>
<defstr>A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>frameshift mutation</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>frameshift sequence variation</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>out of frame mutation</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Frameshift_mutation</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:1000064</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000066</id>
<name>sequence_variant_causing_plus_1_frameshift_mutation</name>
<def>
<defstr>A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>plus 1 frameshift mutation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing plus 1 frameshift mutation</synonym_text>
</synonym>
<is_a>SO:1000065</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000067</id>
<name>sequence_variant_causing_minus_1_frameshift</name>
<def>
<defstr>A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>minus 1 frameshift mutation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing minus 1 frameshift</synonym_text>
</synonym>
<is_a>SO:1000065</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000068</id>
<name>sequence_variant_causing_plus_2_frameshift</name>
<def>
<defstr>A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>plus 2 frameshift mutation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing plus 2 frameshift</synonym_text>
</synonym>
<is_a>SO:1000065</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000069</id>
<name>sequence_variant_causing_minus_2_frameshift</name>
<def>
<defstr>A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>minus 2 frameshift mutation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing minus 2 frameshift</synonym_text>
</synonym>
<is_a>SO:1000065</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000070</id>
<name>sequence_variant_affecting_transcript_processing</name>
<def>
<defstr>Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting transcript processing</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting transcript processing</synonym_text>
</synonym>
<is_a>SO:1000079</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000071</id>
<name>sequence_variant_affecting_splicing</name>
<def>
<defstr>A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting splicing</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting splicing</synonym_text>
</synonym>
<is_a>SO:1000132</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000072</id>
<name>sequence_variant_affecting_splice_donor</name>
<def>
<defstr>A sequence_variant_effect that changes the splice donor sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting splice donor</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>sequence variant affecting splice donor</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>splice donor mutation</synonym_text>
</synonym>
<is_a>SO:1000071</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000073</id>
<name>sequence_variant_affecting_splice_acceptor</name>
<def>
<defstr>A sequence_variant_effect that changes the splice acceptor sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting splicing</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>sequence variant affecting splice acceptor</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>splice acceptor mutation</synonym_text>
</synonym>
<is_a>SO:1000071</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000074</id>
<name>sequence_variant_causing_cryptic_splice_activation</name>
<def>
<defstr>A sequence variant causing a new (functional) splice site.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration.</comment>
<synonym scope="exact">
<synonym_text>cryptic splice activator sequence variant</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>mutation causing cryptic splice activator</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing cryptic splice activator</synonym_text>
</synonym>
<is_a>SO:1000071</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000075</id>
<name>sequence_variant_affecting_editing</name>
<def>
<defstr>Sequence variant affects the editing of the transcript.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting editing</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting editing</synonym_text>
</synonym>
<is_a>SO:1000070</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000076</id>
<name>sequence_variant_affecting_transcription</name>
<def>
<defstr>Mutation affects the process of transcription, its initiation, progression or termination.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting transcription</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting transcription</synonym_text>
</synonym>
<is_a>SO:1000049</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000078</id>
<name>sequence_variant_decreasing_rate_of_transcription</name>
<def>
<defstr>A sequence variation that decreases the rate a which transcription of the sequence occurs.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation decreasing rate of transcription</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variation decreasing rate of transcription</synonym_text>
</synonym>
<is_a>SO:1000081</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000079</id>
<name>sequence_variation_affecting_transcript_sequence</name>
<synonym scope="exact">
<synonym_text>mutation affecting transcript sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variation affecting transcript sequence</synonym_text>
</synonym>
<is_a>SO:1000049</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000080</id>
<name>sequence_variant_increasing_rate_of_transcription</name>
<synonym scope="related">
<synonym_text>mutation increasing rate of transcription</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variation increasing rate of transcription</synonym_text>
</synonym>
<is_a>SO:1000081</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000081</id>
<name>sequence_variant_affecting_rate_of_transcription</name>
<def>
<defstr>A mutation that alters the rate a which transcription of the sequence occurs.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting rate of transcription</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting rate of transcription</synonym_text>
</synonym>
<is_a>SO:1000076</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000082</id>
<name>sequence variant_affecting_transcript_stability</name>
<def>
<defstr>Sequence variant affects the stability of the transcript.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting transcript stability</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting transcript stability</synonym_text>
</synonym>
<is_a>SO:1000079</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000083</id>
<name>sequence_variant_increasing_transcript_stability</name>
<def>
<defstr>Sequence variant increases the stability (half-life) of the transcript.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation increasing transcript stability</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant increasing transcript stability</synonym_text>
</synonym>
<is_a>SO:1000082</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000084</id>
<name>sequence_variant_decreasing_transcript_stability</name>
<def>
<defstr>Sequence variant decreases the stability (half-life) of the transcript.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation decreasing transcript stability</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant decreasing transcript stability</synonym_text>
</synonym>
<is_a>SO:1000082</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000085</id>
<name>sequence_variation_affecting_level_of_transcript</name>
<def>
<defstr>A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting level of transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variation affecting level of transcript</synonym_text>
</synonym>
<is_a>SO:1000049</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000086</id>
<name>sequence_variation_decreasing_level_of_transcript</name>
<def>
<defstr>A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mutation decreasing level of transcript</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>sequence variation decreasing level of transcript</synonym_text>
</synonym>
<is_a>SO:1000085</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000087</id>
<name>sequence_variation_increasing_level_of_transcript</name>
<def>
<defstr>A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mutation increasing level of transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variation increasing level of transcript</synonym_text>
</synonym>
<is_a>SO:1000085</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000088</id>
<name>sequence_variant_affecting_translational_product</name>
<def>
<defstr>Mutation causes a change in primary translation product of a transcript.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting translational product</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting translational product</synonym_text>
</synonym>
<is_a>SO:1000132</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000089</id>
<name>sequence_variant_causing_no_change_of_translational_product</name>
<def>
<defstr>The sequence variant at RNA level does not lead to any change in polypeptide.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing no change of translational product</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing no change of translational product</synonym_text>
</synonym>
<is_a>SO:1000088</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000090</id>
<name>sequence_variant_causing_uncharacterised_change_of_translational_product</name>
<def>
<defstr>A sequence variant causing an uncharacterized change of translational product.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing uncharacterised change of translational product</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing uncharacterised change of translational product</synonym_text>
</synonym>
<is_a>SO:1000088</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000091</id>
<name>sequence_variant_causing_partially_characterised_change_of_translational_product</name>
<def>
<defstr>A sequence variant causing a partially uncharacterised change in translational product.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>The nature of the mutation event is only partially characterised.</comment>
<synonym scope="related">
<synonym_text>mutation causing partially characterised change of translational product</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing partially characterised change of translational product</synonym_text>
</synonym>
<is_a>SO:1000090</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000092</id>
<name>sequence_variant_causing_complex_change_of_translational_product</name>
<def>
<defstr>Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing complex change of translational product</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing complex change of translational product</synonym_text>
</synonym>
<is_a>SO:1000088</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000093</id>
<name>sequence_variant_causing_amino_acid_substitution</name>
<def>
<defstr>The replacement of a single amino acid by another.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing amino acid substitution</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing amino acid substitution</synonym_text>
</synonym>
<is_a>SO:1000105</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000094</id>
<name>sequence_variant_causing_conservative_amino_acid_substitution</name>
<synonym scope="related">
<synonym_text>mutation causing conservative amino acid substitution</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing conservative amino acid substitution</synonym_text>
</synonym>
<is_a>SO:1000093</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000095</id>
<name>sequence_variant_causing_nonconservative_amino_acid_substitution</name>
<synonym scope="related">
<synonym_text>mutation causing nonconservative amino acid substitution</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing nonconservative amino acid substitution</synonym_text>
</synonym>
<is_a>SO:1000093</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000096</id>
<name>sequence_variant_causing_amino_acid_insertion</name>
<def>
<defstr>The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing amino acid insertion</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing amino acid insertion</synonym_text>
</synonym>
<is_a>SO:1000105</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000097</id>
<name>sequence_variant_causing_amino_acid_deletion</name>
<def>
<defstr>The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing amino acid deletion</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing amino acid deletion</synonym_text>
</synonym>
<is_a>SO:1000105</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000098</id>
<name>sequence_variant_causing_polypeptide_truncation</name>
<def>
<defstr>The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062).</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing polypeptide truncation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing polypeptide truncation</synonym_text>
</synonym>
<is_a>SO:1000105</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000099</id>
<name>sequence_variant_causing_polypeptide_elongation</name>
<def>
<defstr>The extension of the translational product at either (or both) the N-terminus and/or the C-terminus.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing polypeptide elongation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing polypeptide elongation</synonym_text>
</synonym>
<is_a>SO:1000105</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000100</id>
<name>mutation_causing_polypeptide_N_terminal_elongation</name>
<def>
<defstr>.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mutation causing polypeptide N terminal elongation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide N-terminal elongation</synonym_text>
</synonym>
<is_a>SO:1000099</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000101</id>
<name>mutation_causing_polypeptide_C_terminal_elongation</name>
<def>
<defstr>.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mutation causing polypeptide C terminal elongation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide C-terminal elongation</synonym_text>
</synonym>
<is_a>SO:1000099</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000102</id>
<name>sequence_variant_affecting_level_of_translational_product</name>
<synonym scope="related">
<synonym_text>mutation affecting level of translational product</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting level of translational product</synonym_text>
</synonym>
<is_a>SO:1000088</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000103</id>
<name>sequence_variant_decreasing_level_of_translation_product</name>
<synonym scope="related">
<synonym_text>mutationdecreasing level of translation product</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant decreasing level of translation product</synonym_text>
</synonym>
<is_a>SO:1000102</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000104</id>
<name>sequence_variant_increasing_level_of_translation_product</name>
<synonym scope="related">
<synonym_text>mutationt increasing level of translation product</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant increasing level of translation product</synonym_text>
</synonym>
<is_a>SO:1000102</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000105</id>
<name>sequence_variant_affecting_polypeptide_amino_acid_sequence</name>
<synonym scope="related">
<synonym_text>mutation affecting polypeptide amino acid sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting polypeptide amino acid sequence</synonym_text>
</synonym>
<is_a>SO:1000088</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000106</id>
<name>mutation_causing_inframe_polypeptide_N_terminal_elongation</name>
<synonym scope="exact">
<synonym_text>inframe polypeptide N-terminal elongation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>mutation causing inframe polypeptide N terminal elongation</synonym_text>
</synonym>
<is_a>SO:1000100</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000107</id>
<name>mutation_causing_out_of_frame_polypeptide_N_terminal_elongation</name>
<synonym scope="exact">
<synonym_text>mutation causing out of frame polypeptide N terminal elongation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>out of frame polypeptide N-terminal elongation</synonym_text>
</synonym>
<is_a>SO:1000100</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000108</id>
<name>mutaton_causing_inframe_polypeptide_C_terminal_elongation</name>
<synonym scope="exact">
<synonym_text>inframe_polypeptide C-terminal elongation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>mutaton causing inframe polypeptide C terminal elongation</synonym_text>
</synonym>
<is_a>SO:1000101</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000109</id>
<name>mutation_causing_out_of_frame_polypeptide_C_terminal_elongation</name>
<synonym scope="exact">
<synonym_text>mutation causing out of frame polypeptide C terminal elongation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>out of frame polypeptide C-terminal elongation</synonym_text>
</synonym>
<is_a>SO:1000101</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000110</id>
<name>frame_restoring_sequence_variant</name>
<def>
<defstr>A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>frame restoring mutation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>frame restoring sequence variant</synonym_text>
</synonym>
<is_a>SO:1000065</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000111</id>
<name>sequence_variant_affecting_3D_structure_of_polypeptide</name>
<def>
<defstr>A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting 3D structure of polypeptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting 3D structure of polypeptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting 3D-structure of polypeptide</synonym_text>
</synonym>
<is_a>SO:1000088</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000112</id>
<name>sequence_variant_causing_no_3D_structural_change</name>
<synonym scope="related">
<synonym_text>mutation causing no 3D structural change</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing no 3D structural change</synonym_text>
</synonym>
<is_a>SO:1000111</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000113</id>
<name>sequence_variant_causing_uncharacterised_3D_structural_change</name>
<synonym scope="related">
<synonym_text>mutation causing uncharacterised 3D structural change</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing uncharacterised 3D structural change</synonym_text>
</synonym>
<is_a>SO:1000111</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000114</id>
<name>sequence_variant_causing_partially_characterised_3D_structural_change</name>
<synonym scope="related">
<synonym_text>mutation causing partially characterised 3D structural change</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing partially characterised 3D structural change</synonym_text>
</synonym>
<is_a>SO:1000113</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000115</id>
<name>sequence_variant_causing_complex_3D_structural_change</name>
<synonym scope="related">
<synonym_text>mutation causing complex 3D structural change</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing complex 3D structural change</synonym_text>
</synonym>
<is_a>SO:1000111</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000116</id>
<name>sequence_variant_causing_conformational_change</name>
<synonym scope="related">
<synonym_text>mutation causing conformational change</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing conformational change</synonym_text>
</synonym>
<is_a>SO:1000111</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000117</id>
<name>sequence_variant_affecting_polypeptide_function</name>
<synonym scope="related">
<synonym_text>mutation affecting polypeptide function</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting polypeptide function</synonym_text>
</synonym>
<is_a>SO:1000088</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000118</id>
<name>sequence_variant_causing_loss_of_function_of_polypeptide</name>
<synonym scope="related">
<synonym_text>loss of function of polypeptide</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>mutation causing loss of function of polypeptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing loss of function of polypeptide</synonym_text>
</synonym>
<is_a>SO:1000117</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000119</id>
<name>sequence_variant_causing_inactive_ligand_binding_site</name>
<synonym scope="related">
<synonym_text>mutation causing inactive ligand binding site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing inactive ligand binding site</synonym_text>
</synonym>
<is_a>SO:1000118</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000120</id>
<name>sequence_variant_causing_inactive_catalytic_site</name>
<synonym scope="related">
<synonym_text>mutation causing inactive catalytic site</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing inactive catalytic site</synonym_text>
</synonym>
<is_a>SO:1000119</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000121</id>
<name>sequence_variant_causing_polypeptide_localization_change</name>
<synonym scope="related">
<synonym_text>mutation causing polypeptide localization change</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing polypeptide localization change</synonym_text>
</synonym>
<is_a>SO:1000117</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000122</id>
<name>sequence_variant_causing_polypeptide_post_translational_processing_change</name>
<synonym scope="related">
<synonym_text>mutation causing polypeptide post translational processing change</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>polypeptide post-translational processing affected</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing polypeptide post translational processing change</synonym_text>
</synonym>
<is_a>SO:1000117</is_a>
<is_a>SO:1000118</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000123</id>
<name>polypeptide_post_translational_processing_affected</name>
<synonym scope="related">
<synonym_text>polypeptide_post-translational_processing_affected</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000124</id>
<name>sequence_variant_causing_partial_loss_of_function_of_polypeptide</name>
<synonym scope="related">
<synonym_text>mutation causing partial loss of function of polypeptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>partial loss of function of polypeptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing partial loss of function of polypeptide</synonym_text>
</synonym>
<is_a>SO:1000118</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000125</id>
<name>sequence_variant_causing_gain_of_function_of_polypeptide</name>
<synonym scope="exact">
<synonym_text>gain of function of polypeptide</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>mutation causing gain of function of polypeptide</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing gain of function of polypeptide</synonym_text>
</synonym>
<is_a>SO:1000117</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000126</id>
<name>sequence_variant_affecting_transcript_secondary_structure</name>
<def>
<defstr>A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting transcript secondary structure</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting transcript secondary structure</synonym_text>
</synonym>
<is_a>SO:1000079</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000127</id>
<name>sequence_variant_causing_compensatory_transcript_secondary_structure_mutation</name>
<synonym scope="related">
<synonym_text>mutation causing compensatory transcript secondary structure mutation</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing compensatory transcript secondary structure mutation</synonym_text>
</synonym>
<is_a>SO:1000126</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000132</id>
<name>sequence_variant_effect</name>
<def>
<defstr>The effect of a change in nucleotide sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Updated after discussion with Peter Taschner - Feb 09.</comment>
<synonym scope="related">
<synonym_text>sequence variant effect</synonym_text>
</synonym>
<disjoint_from>SO:0000240</disjoint_from>
<disjoint_from>SO:0000400</disjoint_from>
<namespace>sequence</namespace>
<is_root>1</is_root>
</term>
<term>
<id>SO:1000134</id>
<name>sequence_variant_causing_polypeptide_fusion</name>
<synonym scope="related">
<synonym_text>mutation causing polypeptide fusion</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing polypeptide fusion</synonym_text>
</synonym>
<is_a>SO:1000105</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000136</id>
<name>autosynaptic_chromosome</name>
<synonym scope="related">
<synonym_text>(Drosophila)A</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>autosynaptic chromosome</synonym_text>
</synonym>
<is_a>SO:1000183</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000138</id>
<name>homo_compound_chromosome</name>
<synonym scope="exact">
<synonym_text>homo compound chromosome</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>homo-compound chromosome</synonym_text>
</synonym>
<is_a>SO:1000042</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000140</id>
<name>hetero_compound_chromosome</name>
<synonym scope="exact">
<synonym_text>hetero compound chromosome</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>hetero-compound chromosome</synonym_text>
</synonym>
<is_a>SO:1000042</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000141</id>
<name>chromosome_fission</name>
<synonym scope="exact">
<synonym_text>chromosome fission</synonym_text>
</synonym>
<is_a>SO:1000028</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000142</id>
<name>dexstrosynaptic_chromosome</name>
<synonym scope="exact">
<synonym_text>dexstrosynaptic chromosome</synonym_text>
</synonym>
<is_a>SO:1000136</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000143</id>
<name>laevosynaptic_chromosome</name>
<synonym scope="exact">
<synonym_text>laevosynaptic chromosome</synonym_text>
</synonym>
<is_a>SO:1000136</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000144</id>
<name>free_duplication</name>
<synonym scope="exact">
<synonym_text>free duplication</synonym_text>
</synonym>
<is_a>SO:1000037</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000145</id>
<name>free_ring_duplication</name>
<synonym scope="related">
<synonym_text>(Drosophila)R</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>free ring duplication</synonym_text>
</synonym>
<is_a>SO:1000045</is_a>
<is_a>SO:1000144</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000146</id>
<name>complex_chromosomal_mutation</name>
<synonym scope="exact">
<synonym_text>complex chromosomal mutation</synonym_text>
</synonym>
<is_a>SO:1000183</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000147</id>
<name>deficient_translocation</name>
<def>
<defstr>A translocation in which one of the four broken ends loses a segment before re-joining.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)Df</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>(Drosophila)DfT</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>deficient translocation</synonym_text>
</synonym>
<is_a>SO:1000029</is_a>
<is_a>SO:1000044</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000148</id>
<name>inversion_cum_translocation</name>
<def>
<defstr>The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)InT</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>(Drosophila)T</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>inversion cum translocation</synonym_text>
</synonym>
<is_a>SO:1000030</is_a>
<is_a>SO:1000044</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000149</id>
<name>bipartite_duplication</name>
<def>
<defstr>The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)bDp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>bipartite duplication</synonym_text>
</synonym>
<is_a>SO:1000031</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000150</id>
<name>cyclic_translocation</name>
<def>
<defstr>Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>cyclic translocation</synonym_text>
</synonym>
<is_a>SO:1000044</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000151</id>
<name>bipartite_inversion</name>
<def>
<defstr>Three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed).</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)bIn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>bipartite inversion</synonym_text>
</synonym>
<is_a>SO:1000030</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000152</id>
<name>uninverted_insertional_duplication</name>
<def>
<defstr>A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)eDp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>uninverted insertional duplication</synonym_text>
</synonym>
<is_a>SO:1000154</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000153</id>
<name>inverted_insertional_duplication</name>
<def>
<defstr>A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)iDp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>inverted insertional duplication</synonym_text>
</synonym>
<is_a>SO:1000154</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000154</id>
<name>insertional_duplication</name>
<def>
<defstr>A chromosome duplication involving the insertion of a duplicated region.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)Dpp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>insertional duplication</synonym_text>
</synonym>
<is_a>SO:1000037</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000155</id>
<name>interchromosomal_transposition</name>
<synonym scope="related">
<synonym_text>(Drosophila)Tp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>interchromosomal transposition</synonym_text>
</synonym>
<is_a>SO:0000453</is_a>
<is_a>SO:1000031</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000156</id>
<name>inverted_interchromosomal_transposition</name>
<synonym scope="related">
<synonym_text>(Drosophila)iTp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>inverted interchromosomal transposition</synonym_text>
</synonym>
<is_a>SO:1000155</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000157</id>
<name>uninverted_interchromosomal_transposition</name>
<synonym scope="related">
<synonym_text>(Drosophila)eTp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>uninverted interchromosomal transposition</synonym_text>
</synonym>
<is_a>SO:1000155</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000158</id>
<name>inverted_intrachromosomal_transposition</name>
<def>
<defstr>The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)iTp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>inverted intrachromosomal transposition</synonym_text>
</synonym>
<is_a>SO:1000030</is_a>
<is_a>SO:1000041</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000159</id>
<name>uninverted_intrachromosomal_transposition</name>
<def>
<defstr>The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)eTp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>uninverted intrachromosomal transposition</synonym_text>
</synonym>
<is_a>SO:1000041</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000160</id>
<name>unoriented_insertional_duplication</name>
<def>
<defstr>A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)uDp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>unoriented insertional duplication</synonym_text>
</synonym>
<is_a>SO:1000154</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000161</id>
<name>unorientated_interchromosomal_transposition</name>
<synonym scope="related">
<synonym_text>(Drosophila)uTp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>unorientated interchromosomal transposition</synonym_text>
</synonym>
<is_a>SO:1000155</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000162</id>
<name>unorientated_intrachromosomal_transposition</name>
<def>
<defstr>The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)uTp</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>unorientated intrachromosomal transposition</synonym_text>
</synonym>
<is_a>SO:1000041</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000170</id>
<name>uncharacterised_chromosomal_mutation</name>
<synonym scope="exact">
<synonym_text>uncharacterised chromosomal mutation</synonym_text>
</synonym>
<is_a>SO:1000183</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000171</id>
<name>deficient_inversion</name>
<def>
<defstr>Three breaks in the same chromosome; one central region lost, the other inverted.</defstr>
<dbxref>
<acc>reference_manual</acc>
<dbname>FB</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>(Drosophila)Df</synonym_text>
</synonym>
<synonym scope="related">
<synonym_text>(Drosophila)DfIn</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>deficient inversion</synonym_text>
</synonym>
<is_a>SO:1000029</is_a>
<is_a>SO:1000030</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000173</id>
<name>tandem_duplication</name>
<synonym scope="exact">
<synonym_text>tandem duplication</synonym_text>
</synonym>
<is_a>SO:1000038</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000175</id>
<name>partially_characterised_chromosomal_mutation</name>
<synonym scope="exact">
<synonym_text>partially characterised chromosomal mutation</synonym_text>
</synonym>
<is_a>SO:1000170</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000177</id>
<name>sequence_variant_causing_uncharacterised_change_in_transcript</name>
<def>
<defstr>The nature of the mutation event is either uncharacterised or only partially characterised.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing uncharacterised change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing uncharacterised change in transcript</synonym_text>
</synonym>
<is_a>SO:1000049</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000179</id>
<name>sequence_variant_causing_partially_characterised_change_in_transcript</name>
<def>
<defstr>The nature of the mutation event is only partially characterised.</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing partially characterised change in transcript</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing partially characterised change in transcript</synonym_text>
</synonym>
<is_a>SO:1000177</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000180</id>
<name>sequence_variant_affecting_gene_structure</name>
<def>
<defstr>A sequence_variant_effect that changes the gene structure.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation affecting gene structure</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant affecting gene structure</synonym_text>
</synonym>
<is_a>SO:1000132</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000181</id>
<name>sequence_variant_causing_gene_fusion</name>
<def>
<defstr>A sequence_variant_effect that changes the gene structure by causing a fusion to another gene.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causing gene fusion</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causing gene fusion</synonym_text>
</synonym>
<is_a>SO:1000180</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000182</id>
<name>chromosome_number_variation</name>
<def>
<defstr>A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>chromosome number variation</synonym_text>
</synonym>
<is_a>SO:0000240</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000183</id>
<name>chromosome_structure_variation</name>
<synonym scope="exact">
<synonym_text>chromosome structure variation</synonym_text>
</synonym>
<is_a>SO:0000240</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000184</id>
<name>sequence_variant_causes_exon_loss</name>
<def>
<defstr>A sequence variant affecting splicing and causes an exon loss.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causes exon loss</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causes exon loss</synonym_text>
</synonym>
<is_a>SO:1000071</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000185</id>
<name>sequence_variant_causes_intron_gain</name>
<def>
<defstr>A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072).</defstr>
<dbxref>
<acc>http://www.ebi.ac.uk/mutations/recommendations/mutevent.html</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="related">
<synonym_text>mutation causes intron gain</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>sequence variant causes intron gain</synonym_text>
</synonym>
<is_a>SO:1000071</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1000186</id>
<name>sequence_variant_causing_cryptic_splice_donor_activation</name>
<synonym scope="exact">
<synonym_text>sequence variant causing cryptic splice donor activation</synonym_text>
</synonym>
<is_a>SO:1000074</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001186</id>
<name>sequence_variant_causing_cryptic_splice_acceptor_activation</name>
<synonym scope="exact">
<synonym_text>sequence variant causing cryptic splice acceptor activation</synonym_text>
</synonym>
<is_a>SO:1000074</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001187</id>
<name>alternatively_spliced_transcript</name>
<def>
<defstr>A transcript that is alternatively spliced.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>alternatively spliced transcript</synonym_text>
</synonym>
<is_a>SO:0000673</is_a>
<intersection_of>
<to>SO:0000673</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000877</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001188</id>
<name>encodes_1_polypeptide</name>
<def>
<defstr>A gene that is alternately spliced, but encodes only one polypeptide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>encodes 1 polypeptide</synonym_text>
</synonym>
<is_a>SO:0000463</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001189</id>
<name>encodes_greater_than_1_polypeptide</name>
<def>
<defstr>A gene that is alternately spliced, and encodes more than one polypeptide.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>encodes greater than 1 polypeptide</synonym_text>
</synonym>
<is_a>SO:0000463</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001190</id>
<name>encodes_different_polypeptides_different_stop</name>
<def>
<defstr>A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>encodes different polypeptides different stop</synonym_text>
</synonym>
<is_a>SO:1001195</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001191</id>
<name>encodes_overlapping_peptides_different_start</name>
<def>
<defstr>A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>encodes overlapping peptides different start</synonym_text>
</synonym>
<is_a>SO:1001195</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001192</id>
<name>encodes_disjoint_polypeptides</name>
<def>
<defstr>A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>encodes disjoint polypeptides</synonym_text>
</synonym>
<is_a>SO:1001189</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001193</id>
<name>encodes_overlapping_polypeptides_different_start_and_stop</name>
<def>
<defstr>A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>encodes overlapping polypeptides different start and stop</synonym_text>
</synonym>
<is_a>SO:1001195</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001194</id>
<name>alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001195</id>
<name>encodes_overlapping_peptides</name>
<def>
<defstr>A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>encodes overlapping peptides</synonym_text>
</synonym>
<is_a>SO:1001189</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001196</id>
<name>cryptogene</name>
<def>
<defstr>A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0000654</is_a>
<is_a>SO:0001431</is_a>
<intersection_of>
<to>SO:0000654</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000976</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001197</id>
<name>dicistronic_primary_transcript</name>
<def>
<defstr>A primary transcript that has the quality dicistronic.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>dicistronic primary transcript</synonym_text>
</synonym>
<is_a>SO:0000079</is_a>
<is_a>SO:0000631</is_a>
<intersection_of>
<to>SO:0000185</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000879</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001217</id>
<name>member_of_regulon</name>
<synonym scope="exact">
<synonym_text>member of regulon</synonym_text>
</synonym>
<is_a>SO:0000081</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001244</id>
<name>alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping</name>
<synonym scope="related">
<synonym_text>alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping</synonym_text>
</synonym>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001246</id>
<name>CDS_independently_known</name>
<def>
<defstr>A CDS with the evidence status of being independently known.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CDS independently known</synonym_text>
</synonym>
<is_a>SO:0000316</is_a>
<intersection_of>
<to>SO:0000316</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000906</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001247</id>
<name>orphan_CDS</name>
<def>
<defstr>A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>orphan CDS</synonym_text>
</synonym>
<is_a>SO:1001254</is_a>
<intersection_of>
<to>SO:1001254</to>
</intersection_of>
<intersection_of>
<type>has_origin</type>
<to>SO:0000910</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001249</id>
<name>CDS_supported_by_domain_match_data</name>
<def>
<defstr>A CDS that is supported by domain similarity.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CDS supported by domain match data</synonym_text>
</synonym>
<is_a>SO:1001251</is_a>
<intersection_of>
<to>SO:1001251</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000908</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001251</id>
<name>CDS_supported_by_sequence_similarity_data</name>
<def>
<defstr>A CDS that is supported by sequence similarity data.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CDS supported by sequence similarity data</synonym_text>
</synonym>
<is_a>SO:1001254</is_a>
<intersection_of>
<to>SO:0000316</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000907</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001254</id>
<name>CDS_predicted</name>
<def>
<defstr>A CDS that is predicted.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CDS predicted</synonym_text>
</synonym>
<is_a>SO:0000316</is_a>
<intersection_of>
<to>SO:0000316</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000732</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001255</id>
<name>status_of_coding_sequence</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001259</id>
<name>CDS_supported_by_EST_or_cDNA_data</name>
<def>
<defstr>A CDS that is supported by similarity to EST or cDNA data.</defstr>
<dbxref>
<acc>xp</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CDS supported by EST or cDNA data</synonym_text>
</synonym>
<is_a>SO:1001251</is_a>
<intersection_of>
<to>SO:1001251</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000909</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001260</id>
<name>internal_Shine_Dalgarno_sequence</name>
<def>
<defstr>A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria.</defstr>
<dbxref>
<acc>12519954</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>internal Shine Dalgarno sequence</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>internal Shine-Dalgarno sequence</synonym_text>
</synonym>
<is_a>SO:0000243</is_a>
<is_a>SO:1001268</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001261</id>
<name>recoded_mRNA</name>
<def>
<defstr>The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>recoded mRNA</synonym_text>
</synonym>
<is_a>SO:0000234</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000881</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001262</id>
<name>minus_1_translationally_frameshifted</name>
<def>
<defstr>An attribute describing a translational frameshift of -1.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>minus 1 translationally frameshifted</synonym_text>
</synonym>
<is_a>SO:0000887</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001263</id>
<name>plus_1_translationally_frameshifted</name>
<def>
<defstr>An attribute describing a translational frameshift of +1.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>plus 1 translationally frameshifted</synonym_text>
</synonym>
<is_a>SO:0000887</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001264</id>
<name>mRNA_recoded_by_translational_bypass</name>
<def>
<defstr>A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mRNA recoded by translational bypass</synonym_text>
</synonym>
<is_a>SO:1001261</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000886</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001265</id>
<name>mRNA_recoded_by_codon_redefinition</name>
<def>
<defstr>A recoded_mRNA that was modified by an alteration of codon meaning.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>mRNA recoded by codon redefinition</synonym_text>
</synonym>
<is_a>SO:1001261</is_a>
<intersection_of>
<to>SO:0000234</to>
</intersection_of>
<intersection_of>
<type>has_quality</type>
<to>SO:0000882</to>
</intersection_of>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001266</id>
<name>stop_codon_redefinition_as_selenocysteine</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001267</id>
<name>stop_codon_readthrough</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001268</id>
<name>recoding_stimulatory_region</name>
<def>
<defstr>A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA.</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>recoding stimulatory region</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>recoding stimulatory signal</synonym_text>
</synonym>
<is_a>SO:0000836</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001269</id>
<name>four_bp_start_codon</name>
<def>
<defstr>A non-canonical start codon with 4 base pairs.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>4bp start codon</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>four bp start codon</synonym_text>
</synonym>
<is_a>SO:0000680</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001270</id>
<name>stop_codon_redefinition_as_pyrrolysine</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001271</id>
<name>archaeal_intron</name>
<def>
<defstr>An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease.</defstr>
<dbxref>
<acc>9301331</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism.</comment>
<synonym scope="exact">
<synonym_text>archaeal intron</synonym_text>
</synonym>
<is_a>SO:0001216</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001272</id>
<name>tRNA_intron</name>
<def>
<defstr>An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Could be a cross product with Gene ontology, GO:0006388.</comment>
<synonym scope="exact">
<synonym_text>pre-tRNA intron</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>tRNA intron</synonym_text>
</synonym>
<is_a>SO:0001216</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001273</id>
<name>CTG_start_codon</name>
<def>
<defstr>A non-canonical start codon of sequence CTG.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>CTG start codon</synonym_text>
</synonym>
<is_a>SO:0000680</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001274</id>
<name>SECIS_element</name>
<def>
<defstr>The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes.</defstr>
<dbxref>
<acc>http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>SECIS element</synonym_text>
</synonym>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/SECIS_element</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:1001268</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001275</id>
<name>retron</name>
<def>
<defstr>Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes.</defstr>
<dbxref>
<acc>ma</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>SO:0001411</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001277</id>
<name>three_prime_recoding_site</name>
<def>
<defstr>The recoding stimulatory signal located downstream of the recoding site.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>three prime recoding site</synonym_text>
</synonym>
<is_a>SO:1001268</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001279</id>
<name>three_prime_stem_loop_structure</name>
<def>
<defstr>A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region.</defstr>
<dbxref>
<acc>12519954</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>three prime stem loop structure</synonym_text>
</synonym>
<is_a>SO:1001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001280</id>
<name>five_prime_recoding_site</name>
<def>
<defstr>The recoding stimulatory signal located upstream of the recoding site.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>five prime recoding site</synonym_text>
</synonym>
<is_a>SO:1001268</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001281</id>
<name>flanking_three_prime_quadruplet_recoding_signal</name>
<def>
<defstr>Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons.</defstr>
<dbxref>
<acc>12519954</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>flanking three prime quadruplet recoding signal</synonym_text>
</synonym>
<is_a>SO:1001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001282</id>
<name>UAG_stop_codon_signal</name>
<def>
<defstr>A stop codon signal for a UAG stop codon redefinition.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>UAG stop codon signal</synonym_text>
</synonym>
<is_a>SO:1001288</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001283</id>
<name>UAA_stop_codon_signal</name>
<def>
<defstr>A stop codon signal for a UAA stop codon redefinition.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>UAA stop codon signal</synonym_text>
</synonym>
<is_a>SO:1001288</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001284</id>
<name>regulon</name>
<def>
<defstr>A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal.</defstr>
<dbxref>
<acc>0198506732</acc>
<dbname>ISBN</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<xref_analog>
<acc>http://en.wikipedia.org/wiki/Regulon</acc>
<dbname>URL</dbname>
<name>wiki</name>
</xref_analog>
<is_a>SO:0005855</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001285</id>
<name>UGA_stop_codon_signal</name>
<def>
<defstr>A stop codon signal for a UGA stop codon redefinition.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>UGA stop codon signal</synonym_text>
</synonym>
<is_a>SO:1001288</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001286</id>
<name>three_prime_repeat_recoding_signal</name>
<def>
<defstr>A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.</defstr>
<dbxref>
<acc>12519954</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>three prime repeat recoding signal</synonym_text>
</synonym>
<is_a>SO:1001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001287</id>
<name>distant_three_prime_recoding_signal</name>
<def>
<defstr>A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon.</defstr>
<dbxref>
<acc>http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<synonym scope="exact">
<synonym_text>distant three prime recoding signal</synonym_text>
</synonym>
<is_a>SO:1001277</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:1001288</id>
<name>stop_codon_signal</name>
<def>
<defstr>A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding.</defstr>
<dbxref>
<acc>12519954</acc>
<dbname>PMID</dbname>
</dbxref>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal.</comment>
<synonym scope="exact">
<synonym_text>stop codon signal</synonym_text>
</synonym>
<is_a>SO:1001268</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:2000061</id>
<name>databank_entry</name>
<def>
<defstr>The sequence referred to by an entry in a databank such as Genbank or SwissProt.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<synonym scope="related">
<synonym_text>accession</synonym_text>
</synonym>
<synonym scope="exact">
<synonym_text>databank entry</synonym_text>
</synonym>
<is_a>SO:0000695</is_a>
<namespace>sequence</namespace>
</term>
<term>
<id>SO:3000000</id>
<name>gene_segment</name>
<def>
<defstr>A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.</defstr>
<dbxref>
<acc>add</acc>
<dbname>GOC</dbname>
</dbxref>
</def>
<comment>Requested by tracker 2021594, July 2008, by Alex.</comment>
<synonym scope="exact">
<synonym_text>gene segment</synonym_text>
</synonym>
<is_a>SO:0000842</is_a>
<namespace>sequence</namespace>
</term>
<typedef>
<id>adjacent_to</id>
<name>adjacent_to</name>
<def>
<defstr>A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>associated_with</id>
<name>associated_with</name>
<comment>This relationship is vague and up for discussion.</comment>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>complete_evidence_for_feature</id>
<name>complete_evidence_for_feature</name>
<def>
<defstr>B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.</comment>
<is_transitive>1</is_transitive>
<is_a>evidence_for_feature</is_a>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>derives_from</id>
<name>derives_from</name>
<subset>SOFA</subset>
<is_transitive>1</is_transitive>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>edited_from</id>
<name>edited_from</name>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T02:19:45Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>edited_to</id>
<name>edited_to</name>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T02:19:11Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>evidence_for_feature</id>
<name>evidence_for_feature</name>
<def>
<defstr>B is evidence_for_feature A, if an instance of B supports the existence of A.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.</comment>
<is_transitive>1</is_transitive>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>exemplar_of</id>
<name>exemplar_of</name>
<def>
<defstr>X is exemplar of Y if X is the best evidence for Y.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Tracker id: 2594157.</comment>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>genome_of</id>
<name>genome_of</name>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>guided_by</id>
<name>guided_by</name>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T02:27:04Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>guides</id>
<name>guides</name>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T02:27:24Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>has_genome_location</id>
<name>has_genome_location</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>has_intergral_part</id>
<name>has_integral_part</name>
<def>
<defstr>X has_integral_part Y if and only if: X has_part Y and Y part_of X.</defstr>
<dbxref>
<acc>http://precedings.nature.com/documents/3495/version/1</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Example: mRNA has_integral_part CDS.</comment>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T12:01:46Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>has_origin</id>
<name>has_origin</name>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>has_part</id>
<name>has_part</name>
<def>
<defstr>Inverse of part_of.</defstr>
<dbxref>
<acc>http://precedings.nature.com/documents/3495/version/1</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Example: operon has_part gene.</comment>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>has_quality</id>
<name>has_quality</name>
<comment>The relationship between a feature and an attribute.</comment>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>homologous_to</id>
<name>homologous_to</name>
<subset>SOFA</subset>
<is_symmetric>1</is_symmetric>
<is_a>similar_to</is_a>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>integral_part_of</id>
<name>integral_part_of</name>
<def>
<defstr>X integral_part_of Y if and only if: X part_of Y and Y has_part X.</defstr>
<dbxref>
<acc>http://precedings.nature.com/documents/3495/version/1</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Example: exon integral_part_of transcript.</comment>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T12:03:28Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>member_of</id>
<name>member_of</name>
<comment>A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.</comment>
<subset>SOFA</subset>
<is_transitive>1</is_transitive>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>non_functional_homolog_of</id>
<name>non_functional_homolog_of</name>
<def>
<defstr>A relationship between a pseudogenic feature and its functional ancestor.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<subset>SOFA</subset>
<is_a>homologous_to</is_a>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>orthologous_to</id>
<name>orthologous_to</name>
<subset>SOFA</subset>
<is_symmetric>1</is_symmetric>
<is_a>homologous_to</is_a>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>paralogous_to</id>
<name>paralogous_to</name>
<subset>SOFA</subset>
<is_symmetric>1</is_symmetric>
<is_a>homologous_to</is_a>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>OBO_REL:part_of</id>
<name>part_of</name>
<def>
<defstr>X part_of Y if X is a subregion of Y.</defstr>
<dbxref>
<acc>http://precedings.nature.com/documents/3495/version/1</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Example: amino_acid part_of polypeptide.</comment>
<subset>SOFA</subset>
<is_transitive>1</is_transitive>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>partial_evidence_for_feature</id>
<name>partial_evidence_for_feature</name>
<def>
<defstr>B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.</defstr>
<dbxref>
<acc>ke</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<is_a>evidence_for_feature</is_a>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>position_of</id>
<name>position_of</name>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>processed_from</id>
<name>processed_from</name>
<def>
<defstr>Inverse of processed_into.</defstr>
<dbxref>
<acc>http://precedings.nature.com/documents/3495/version/1</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Example: miRNA processed_from miRNA_primary_transcript.</comment>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T12:14:00Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>processed_into</id>
<name>processed_into</name>
<def>
<defstr>X is processed_into Y if a region X is modified to create Y.</defstr>
<dbxref>
<acc>http://precedings.nature.com/documents/3495/version/1</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Example: miRNA_primary_transcript processed into miRNA.</comment>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T12:15:02Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>recombined_from</id>
<name>recombined_from</name>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T02:21:03Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>recombined_to</id>
<name>recombined_to</name>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T02:20:07Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>regulated_by</id>
<name>regulated_by</name>
<is_obsolete>1</is_obsolete>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>sequence_of</id>
<name>sequence_of</name>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>similar_to</id>
<name>similar_to</name>
<subset>SOFA</subset>
<is_symmetric>1</is_symmetric>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>trans_spliced_from</id>
<name>trans_spliced_from</name>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T02:22:14Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>trans_spliced_to</id>
<name>trans_spliced_to</name>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T02:22:00Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>transcribed_from</id>
<name>transcribed_from</name>
<def>
<defstr>X is transcribed_from Y if X is synthesized from template Y.</defstr>
<dbxref>
<acc>http://precedings.nature.com/documents/3495/version/1</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Example: primary_transcript transcribed_from gene.</comment>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T12:05:39Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>transcribed_to</id>
<name>transcribed_to</name>
<def>
<defstr>Inverse of transcribed_from.</defstr>
<dbxref>
<acc>http://precedings.nature.com/documents/3495/version/1</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Example: gene transcribed_to primary_transcript.</comment>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T12:08:24Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>translates_to</id>
<name>translates_to</name>
<def>
<defstr>Inverse of translation _of.</defstr>
<dbxref>
<acc>http://precedings.nature.com/documents/3495/version/1</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Example: codon translates_to amino_acid.</comment>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T12:11:53Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>translation_of</id>
<name>translation_of</name>
<def>
<defstr>X is translation of Y if X is translated by ribosome to create Y.</defstr>
<dbxref>
<acc>http://precedings.nature.com/documents/3495/version/1</acc>
<dbname>URL</dbname>
</dbxref>
</def>
<comment>Example: Polypeptide translation_of CDS.</comment>
<created_by>kareneilbeck</created_by>
<creation_date>2009-08-19T12:09:59Z</creation_date>
<namespace>sequence</namespace>
</typedef>
<typedef>
<id>variant_of</id>
<name>variant_of</name>
<def>
<defstr>A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.</defstr>
<dbxref>
<acc>immuno_workshop</acc>
<dbname>SO</dbname>
</dbxref>
</def>
<comment>Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.</comment>
<namespace>sequence</namespace>
</typedef>
</obo>